Before patients trust your app with their health, they need to trust you with their data. HIPAA is how you earn that trust. In 2025, building a HIPAA compliant app is the foundation of credibility for any mobile health or research platform. For universities, hospitals, and grant-funded teams, the stakes are exceptionally high. A single misstep can trigger lawsuits or jeopardize funding. It can also damage an institution’s reputation.
According to the latest data, the OCR Data breach portal reports 725 major healthcare data breaches (breaches that affect 500 people or more) in 2024. The number of records exposed, stolen, or impermissibly disclosed has also been increasing rapidly since 2022. In 2024, more than 275 million healthcare records were affected. Two of the top four biggest healthcare data breaches ever occurred in 2024. These statistics underscore the urgency of proactive compliance.
For research teams, early compliance signals responsible stewardship of public funds and increases the likelihood of IRB approval, and for institutions, it serves as a safeguard against reputational and financial risk. Patients using HIPAA compliant apps can rest assured that their data is safe and secure.
We’ve seen first hand how projects falter when clinicians and researchers treat HIPAA as an afterthought. Delaying compliance until late-stage development often leads to costly rework and design and architectural compromises. That’s why we always recommend that our customers complete a HIPAA compliant app launch checklist at the very beginning of a project. It’s about building with integrity, not scrambling under pressure.
This guide distills what we’ve learned from years of supporting healthcare innovators and developing HIPAA compliant apps. The goal is to help you understand the crucial role that HIPAA compliance plays in building apps that meet regulatory standards, protect patient data, earn stakeholder trust, and stand the test of time.
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Download MindSea’s checklist to identify which PHI your app may collect, confirm technical safeguards, and ask the right questions to vet your development partner before launch.
Table of contents
- What is HIPAA, and who does it apply to?
- HIPAA compliance for app development: four rules you can’t ignore
- Implement technical safeguards
- Establish administrative and organizational safeguards
- Consider physical safeguards and hosting environments
- Integrate UX and research-specific considerations
- Avoid common mistakes and red flags
- Understand the costs and timelines of HIPAA compliance
- A step-by-step: Building a HIPAA compliant app launch checklist
- Choosing a HIPAA compliant app partner
- The blueprint for responsible HIPAA implementation
What is HIPAA, and who does it apply to?
The Health Insurance Portability and Accountability Act (HIPAA) is a U.S. federal law that establishes the rules for the handling of protected health information (PHI) across digital and physical systems. HIPAA governs the full lifecycle of data handling, from initial architecture and vendor selection to breach response and offboarding.
According to the HSS, HIPAA applies when research involves PHI and is conducted by or on behalf of a covered entity, regardless of whether:
- The study is federally funded
- The data is collected directly or indirectly
- The app is used in clinical care or research settings
Along with covered entities (such as hospitals, insurers, academic medical centers, physicians, and research institutions), HIPAA also applies to business associates (such as app developers handling PHI on their behalf) and subcontractors who support those vendors. It also applies across jurisdictions if U.S. patients or systems are involved, even when the app is developed or hosted outside the U.S.
What is PHI?
Understanding what constitutes PHI can be confusing. Data such as heart rate, mood tracking, or medication reminders may seem benign, but when tied to an individual and used in a healthcare context, it becomes regulated.
PHI refers to any health-related data that can identify a person, either directly (such as a name or medical record number) or indirectly (such as a device ID or location). It’s not just about clinical records; even behavioral or biometric data becomes PHI when linked to identity and used by a covered entity. That means apps collecting sleep patterns, glucose levels, or symptom logs may be subject to HIPAA even if they never mention diagnoses. Context, identifiability, intent, and the covered entity relationship are the factors that trigger regulation.
When an app manages identifiable health information on behalf of a covered entity, it becomes subject to the four HIPAA compliance rules. Apps for remote patient monitoring, clinical research, and digital therapy all must be compliant with HIPAA regulations. But even wellness apps may require HIPAA compliance if they interface with covered entities, sync with EHR systems, or collect data that can be linked to an individual. The determining factor isn’t the app’s category but whether PHI is created, received, maintained, or transmitted in connection with a covered entity’s operations.To navigate this sometimes confusing landscape, you need to understand the four key HIPAA rules that shape technical and operational decisions.
HIPAA compliance for app development: four rules you can’t ignore
HIPAA includes four key rules, which each govern a different aspect of how to handle PHI and have implications for the design of mobile apps. These are:
- Privacy Rule
- Security Rule
- Breach Notification Rule
- Omnibus Rule
Here’s a breakdown of what each rule means for app development, and how to address it proactively:
| HIPAA Rule | What It Means for Digital Health Apps | Practical Examples |
|---|---|---|
| Privacy Rule | Limit access to PHI and define who can view what | Role-based permissions for researchers vs. participants |
| Security Rule | Protect PHI with technical safeguards | End-to-end encryption, secure login, and audit logging |
| Breach Notification Rule | Notify users and authorities if PHI is compromised | Automated alerts and breach response workflow |
| Omnibus Rule | Extend HIPAA obligations to vendors and subcontractors | Signed BAAs, secure data handling across third-party tools |
In our experience with MindSea clients, the Privacy Rule tends to be more intuitive, as most healthcare professionals understand the importance of confidentiality.
The Security Rule and Breach Notification Rule are where teams often stumble as they underestimate their complexity. These two rules involve technical decisions regarding encryption and access controls, which are areas that may fall outside the expertise of researchers or institutional leads.
The Breach Notification Rule can be difficult to understand, as it’s not always clear what constitutes a breach, and the thresholds for reporting can be nuanced. Some institutions have robust internal protocols and strong in-house support for managing breach notifications, while others have to try to navigate this ambiguity on the fly and on their own.
Audit logging, which is a part of the Security Rule, is also a common oversight. HIPAA requires audit logging for all system users who access PHI. The system must record who accessed or viewed patient data, when the access occurred, and whether any changes were made. This is a core safeguard under the Security Rule. We’ve seen teams dismiss this as irrelevant only to find out that it’s a non-negotiable requirement. Building this functionality retroactively is costly and disruptive.
Privacy Rule Updates
In August 2025, the Office for Civil Rights (OCR) released a new FAQ clarifying how the HIPAA Privacy Rule applies to disclosures of PHI for value-based care arrangements, such as treatment coordination between providers. At the same time, OCR updated an existing FAQ on individuals’ right of access to their health information, expanding the examples of what must be provided, such as signed consent forms.
These updates do not broadly redefine HIPAA applicability to third-party apps, but they do reinforce how important it is to understand how to share and access PHI across digital platforms and the technical safeguards that must be in place to support that access.
Implement technical safeguards
As healthcare technology advances, new security challenges emerge, which makes technical safeguards more important than ever. Healthcare organizations need to protect electronic health information from both internal and external risks, and HIPAA’s Security Rule lays out the standards for doing so.
These safeguards aren’t tied to specific tools or platforms. Instead, the Security Rule provides organizations with flexibility to choose security measures that are reasonable and appropriate for their specific setup. That means each covered entity must decide which technologies and policies make sense for their environment, as long as they meet the core requirements. The Rule is about protecting sensitive data without locking organizations into rigid tech choices and doing so in a way that scales with change.
When building HIPAA compliant digital health tools, there are five core technical safeguards that must be in place:
- Access controls
Covered entities must implement policies and procedures to ensure that only authorized individuals and systems can access electronic protected health information (ePHI). This includes unique user IDs, emergency access procedures, automatic logoff, and encryption and decryption.
- Audit controls
Systems must have mechanisms to record and examine access and activity involving ePHI. These controls help detect unauthorized access and support investigations. Modern solutions, such as AWS CloudTrail, offer real-time monitoring, not just retrospective review.
- Integrity
Measures must be in place to ensure ePHI is not improperly altered or destroyed. This includes mechanisms to verify data integrity and assigning least-privilege or read-only access where possible.
- Person or entity authentication
Procedures must verify that the person or entity accessing ePHI is who they claim to be. This goes beyond simple passwords to include stronger methods such as electronic signatures, callbacks, or multi-factor authentication.
- Transmission security
ePHI transmitted over electronic networks must be protected against unauthorized access. While the original rule was written in the dial-up era, today this means implementing encryption and integrity controls for internet-based communications.
While technical safeguards protect the system itself, they must be reinforced by administrative and organizational safeguards, including policies, procedures, training, and agreements that govern how people interact with PHI. Without these, even the most secure infrastructure can be vulnerable to compromise.
Clarifying HIPAA obligations during a hospital RFP process
In one RFP with a major hospital system, the team behind it was struggling to secure funding to address the compliance gaps. Their approach was to defer HIPAA implementation and treat it as something optional that could be added later. That mindset puts them at real legal risk. Our role was to communicate the seriousness of those implications and ensure they understood that HIPAA is a regulatory obligation, not a feature to toggle on when convenient.
We’ve developed a custom technology stack that aligns with HIPAA standards, along with templates that allow new projects to launch with default configurations that meet compliance expectations. We begin every one of our HIPAA-related builds with secure defaults. Our structured onboarding process ensures that we make all technical decisions – such as hosting, architecture, and data handling – with HIPAA in mind from the outset.
Establish administrative and organizational safeguards
Administrative and organizational safeguards are where HIPAA compliance becomes operational. They govern how people, vendors, and processes interact with protected health information, and they’re just as critical as technical infrastructure and safeguards.
These safeguards form the backbone of HIPAA’s Security Rule, which requires covered entities to put in place clear policies and procedures to guard against and react to security incidents. They begin with a Security Management Process. This includes:
- Ongoing risk analysis
- Risk management
- Sanctions for non-compliance
- Routine reviews of system activity
Organizations must also assign a security official to develop and implement the policies and procedures required by the Security Rule and prevent inappropriate access.
Training is another important administrative safeguard. Organizations need a continuous Security Awareness and Training program that addresses password protection, malicious software, log-in monitoring, and periodic security reminders. Entities must also maintain Security Incident Procedures to detect, document, and respond to breaches, alongside Contingency Plans to ensure critical data can be recovered and operations sustained during emergencies.
Regular evaluations also help verify that safeguards remain effective amid technological or organizational change.
We guide clients through these requirements using a structured HIPAA compliant app launch checklist. Business Associate Agreements (BAAs) are a crucial component of this process. Staff training and internal policies are also covered in our onboarding process. These elements are often overlooked in early planning, especially in grant-funded projects where budgets may not account for the full scope of HIPAA compliance.
What is a Business Associate Agreement (BAA)?
A BAA is a legal requirement under HIPAA whenever a vendor handles PHI on behalf of a healthcare organization. It outlines what the vendor is allowed to do with that data and what safeguards they’re expected to have in place. BAAs serve as a formal agreement that defines accountability and risk boundaries across the project. In these agreements, MindSea clarifies where our responsibilities as a development partner end and where the client’s responsibilities as the data custodian begin.
Sharing PHI with a vendor without a BAA counts as a HIPAA violation. While signing one doesn’t automatically make a vendor HIPAA compliant, it’s a key part of the overall compliance picture.
HIPAA also requires organizations to formalize these safeguards through organizational policies, procedures, and documentation. Every covered entity must implement and maintain written policies that define how security measures are carried out, reviewed, and updated as operations evolve. Documentation (which must be kept for at least six years) needs to be readily available to those responsible for compliance and updated whenever technology, structure, or risk change.
In practice, this documentation turns compliance into a day-to-day structure. These safeguards provide teams with clear guidance on managing PHI and their overall security responsibilities.
Incident response and breach notifications are the next line of defence. Under the HIPAA Breach Notification Rule, any impermissible use or disclosure of PHI must be evaluated to determine if it constitutes a breach. If so, covered entities are legally required to notify affected individuals, HHS, and, in some cases, the media. That’s why we encourage clients to build response protocols early, before they’re needed. This is a crucial link between administrative planning and the technical and physical controls that follow.
Consider physical safeguards and hosting environments
Physical safeguards are often overlooked in digital health projects, but they’re a core component of HIPAA compliance, especially when it comes to hosting environments and device-level risks. HIPAA’s Physical Safeguards cover four key areas:
- Facility access controls
- Workstation use
- Workstation security
- Device and media controls
These safeguards require policies that clearly define how facilities are accessed. They also set standards for securing workstations and for the proper management of hardware or media containing PHI, including how they are reused or disposed of. In hosting environments, this also extends to physical data centers, where access procedures, maintenance logs, and contingency plans must be documented and tested. Even in cloud-based systems, covered entities are responsible for confirming that providers apply equivalent protections at the physical layer. This ranges from secured server rooms to proper destruction of retired storage devices.
Choosing a hosting provider that understands HIPAA requirements can reduce risk and simplify compliance. It also creates a more secure foundation for digital health tools.. However, using a HIPAA compliant host doesn’t automatically make your app or system compliant. The responsibility for proper configuration, access management, and ongoing monitoring still lies with the covered entity or business associate.
Which cloud hosting provider do you recommend?
At MindSea, our go-to hosting provider is AWS, though we work equally well with Google Cloud and Microsoft Azure. These platforms offer HIPAA-aligned services and make it straightforward to enter into BAAs. That said, one common misconception is that services within these platforms are HIPAA compliant by default, which is not the case. Only eligible services from these cloud providers are compatible with HIPAA.
We’ve encountered clients using on-premises infrastructure under the assumption that in-house equals more secure. Keeping data within your own doors feels more secure, and sometimes it is, but it’s certainly not always the case. In reality, maintaining physical access controls and managing security updates internally can be far more complex and resource-intensive. Without the right expertise and protocols, these setups can introduce significant risk.
Device-level exposure is another area that requires careful analysis. Institutional users, such as researchers or clinicians, are typically governed by internal policies that prevent them from using of jailbroken or rooted devices. For patient-facing apps, the situation varies. Some patients use their own devices, while others receive institutionally managed ones. In either case, a custom risk assessment is essential to determine how and where PHI might be exposed.
Integrate UX and research-specific considerations
Even with secure infrastructure and compliant hosting, HIPAA risks can surface through poor UX decisions, especially in patient-facing apps and research tools. Physical safeguards may protect the data, but if users can’t understand how to manage it, compliance falters.
What UX pitfalls can derail compliance?
One common pitfall is treating compliance-related elements as afterthoughts. We’ve seen projects where terms and conditions were added late in the design process, leaving patients confused about how to request or delete their data. These elements must be designed in from the start.
Research shows that patients often feel overwhelmed by the dense, legalistic language used in informed consent forms. In a NIH study, participants expressed a strong preference for plain language, visual aids, extended informed consent discussions, and test/feedback techniques that allowed them to explore details at their own pace. Many described current consent processes as too long, too complicated, or not written for patients. This is both a usability and trust issue, as patient confidence is earned through thoughtful design.
How do you balance compliance with usability and patient-friendliness?
Balancing usability with legal requirements is often straightforward for patients, since most HIPAA protections operate behind the scenes. However, for clinicians, it can be more challenging to explain why specific data is hidden or restricted. To that end, we offer a service at the beginning of a project where we:
- Interview 5 to 10 potential users
- Discuss some of their needs and concerns
- Surface their expectations and clarify what’s medically necessary versus legally permissible
In research contexts, informed consent adds another layer. A common misconception is that patients can “consent away” HIPAA obligations, but HIPAA is statutory, and consent does not equal compliance.
Avoid common mistakes and red flags
When scoping a HIPAA project, the number one red flag is when a client already has an app that’s clearly out of alignment with HIPAA, and they’re unaware of the deficiency. That lack of awareness signals deeper gaps in understanding and risk management.
Another warning sign is when the client wants to collect a large amount of data, typically because they want to use it to power an AI feature in the future. While the ambition is understandable, it dramatically increases the surface area of risk. More data points increase the complexity of managing compliance effectively.
Other common missteps include:
- Assuming HIPAA is “just encryption”
- Overlooking data retention and deletion policies
- Using offshore developers without clear jurisdictional safeguards
- Underestimating ongoing audits
Understand the costs and timelines of HIPAA compliance
Each phase of the HIPAA roadmap carries real implications for budget and timeline. Whether you’re working within institutional constraints or fixed grant funding, understanding the cost and time demands of compliance is essential to scoping realistically and avoiding derailment later on.
What does developing a HIPAA compliant app cost, and how do you budget for it?
Based on our experience building HIPAA compliant apps, the total price typically falls between $75,000 and $400,000 USD, depending on your specific project complexity and integrations requirements, with additional annual maintenance costs of $4,000 to $12,000 per year.
Beyond product development, full organizational compliance introduces its own financial demands. Secureframe reports that implementing HIPAA across an organization can cost anywhere from $25,000 to over $100,000 USD, depending on the size of the entity and the volume of protected health information handled. This includes risk assessments, audits, remediation, staff training, and cybersecurity infrastructure.
Even routine internal audits incur significant costs. Axeleos notes that risk assessments alone can cost $5,000 to $20,000 USD and must be repeated every year to remain compliant with the HIPAA Security Rule. These costs cover the time spent by compliance officers, IT staff, and external auditors who thoroughly review security protocols, policies, and IT infrastructure.
HIPAA compliance cost breakdown
| Cost component | Cost range (USD) | Source |
|---|---|---|
| App development | $75,000 – $400,000 | Based on MindSea projects |
| Annual maintenance | $4,000 – $12,000 | Based on MindSea projects |
| Full organizational compliance | $25,000 – $100,000+ | Secureframe |
| Internal risk assessments | $5,000 – $20,000 annually | Axeleos |
These figures often don’t account for hidden costs, such as the time and effort needed to align stakeholders and drive workflow changes across teams. They also don’t reflect the cost and risk of non-compliance, whether that’s through fines, reputational damage, or operational disruption. Scoping accurately means budgeting not just for setup, but for continued management.
As compliance is a table-stakes requirement, our approach is to embed it in the architecture, workflows, and deployment strategy from day one. That’s why we estimate projects using a ROM (range of magnitude) that reflects healthcare-grade development.
How do you set timeline expectations with grant-funded projects?
For grant-funded teams, the challenge is scope flexibility. With fixed budgets and rigid timelines, we use an agile approach to define a minimal viable product that includes all mandatory HIPAA protections, while allowing feature decisions to evolve.
Weekly check-ins help teams track progress and make informed trade-offs. This ensures:
- Core compliance is never compromised
- Features are prioritized based on funding realities
- Roadmaps adapt without losing integrity
With tight funding, transparency and trust are essential. We work closely with clients to ensure every decision is grounded in shared priorities and that there are no surprises.
A step-by-step: Building a HIPAA compliant app launch checklist
HIPAA compliance is a phased process that we embed into every stage of development. We guide clients through a four-phase roadmap based on our HIPAA onboarding checklist. This helps teams anticipate risks and build safeguards into both the product and the process.
Get Your Free HIPAA Compliant App Launch Checklist
Download MindSea’s checklist to identify which PHI your app may collect, confirm technical safeguards, and ask the right questions to vet your development partner before launch.
We find that healthcare organizations often struggle in Phase 1, where they must identify and document all the PHI that their app will handle. It’s easy to underestimate what qualifies as PHI, especially when dealing with metadata or indirect identifiers. We point our clients to resources like the CPHS list of 18 HIPAA identifiers to clarify what’s in scope.
The second common challenge is budgeting and timeline planning for security requirements. You must bake these safeguards into the architecture, not treat them as bolt-ons. We guide clients through these sticking points with open and collaborative communication, which builds shared understanding and trust.
HIPAA compliant app launch checklist
Each of the four distinct phases of our checklist includes key actions, a suggested timeline, a status box, and a clear owner.
| Phase | Key actions | Owner |
| 1. Project Kickoff | BAA setup, subcontractor list, PHI mapping, data flow review, risk analysis | Shared |
| 2. Technical Safeguards | MFA, encryption, audit logging, budget allocation, IT alignment | MindSea |
| 3. Admin & Physical Setup | HIPAA training, access documentation, breach planning, hosting compliance | Shared |
| 4. Deployment & Ongoing | De-identified test data, compliance reviews, recordkeeping, reassessments | Client (with support) |
Choosing a HIPAA compliant app partner
When you’re looking for a HIPAA compliant app development partner, you need to think about technical skill, along with trust and transparency. One of the clearest indicators of this is whether a vendor is prepared to sign a BAA. If they hesitate or suggest that patient consent can override HIPAA obligations, that’s a red flag. It’s also essential to ask which cloud services they consider HIPAA-eligible and whether they can back up their claims with real case studies.
Industry experience is also essential. Unlike agencies that list healthcare as one of many verticals, MindSea exclusively focuses on health, wellness, and medical apps. That singular focus gives us deep expertise, not just in HIPAA, but in the broader regulatory and organizational realities of healthcare innovation. Clients benefit from hard-earned lessons across dozens of similar projects, helping them avoid common pitfalls and botched implementations.
The blueprint for responsible HIPAA implementation
HIPAA compliance is a foundational responsibility when building digital health tools. From encryption and access controls to audit logging and secure data transmission, every safeguard matters. The stakes are high, and shortcuts lead to risk, not speed.
If we had one piece of advice for a research team or university starting to design and build their first HIPAA compliant app, it would be this: do a thorough project analysis before writing a single line of code. We facilitate this process through our Blueprint service, which allows us to fully design the app and surface all project risks before development begins. Most first-time teams skip this step and dive into build mode with a lot of assumptions, and that’s where costly mistakes happen.
If you’re building something that handles health data, start with clarity. Begin by mapping potential risks and defining boundaries. Then focus on building the system correctly from day one. HIPAA compliance isn’t just about secure systems. It’s about building a culture of responsibility around health data.
Key Takeaways
- HIPAA compliance is foundational, not optional: Integrating requirements early protects patient data and ensures the project aligns with regulatory standards. It also demonstrates reliability to users and institutions.
- Planning early reduces risks and costly mistakes: Identifying PHI and evaluating potential vulnerabilities before development allows the workflow to incorporate necessary protections and avoids rework or legal complications.
- Technical, administrative, and physical safeguards are all essential: Compliance isn’t just about encryption. It also requires secure infrastructure, clear policies, trained personnel, and proper hosting and device management.
Choosing the right partner and process matters: Working with experienced vendors and establishing clear responsibilities through agreements supports long-term security and the longevity of your digital health tools.
