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April 28, 2025

Designing a HIPAA-Compliant Cloud Architecture for Healthcare Apps on AWS

Introduction

Healthcare software requires more than performance and scale—it demands airtight security and compliance. HIPAA regulations define how Protected Health Information (PHI) should be handled, requiring encryption, access controls, audit logging, and incident response. Fortunately, AWS provides a robust set of services and tools that—when architected correctly—enable teams to build secure, HIPAA-compliant applications.

This guide outlines a comprehensive architecture for building HIPAA-ready backend infrastructure on AWS. It’s designed for CTOs, healthcare founders, and engineering leaders who need to ensure their applications comply with HIPAA without compromising developer velocity. For deeper dive into the architecture read our follow up blog post: HIPAA-Compliant Cloud Architecture Deep Dive.

Understanding HIPAA and AWS Compliance

HIPAA mandates a set of administrative, physical, and technical safeguards for protecting Protected Health Information (PHI). These are codified primarily through the Privacy Rule, Security Rule, and Breach Notification Rule. For organizations building healthcare applications, compliance means not only securing PHI but also demonstrating due diligence in how systems are architected and operated.

AWS enables HIPAA-compliant workloads through a Business Associate Addendum (BAA)—a legal agreement required before any PHI can be processed on the platform. Once in place, customers may use a defined set of HIPAA-eligible AWS services to store, transmit, or process PHI. This includes services such as Amazon EC2, Amazon S3, Amazon RDS, Lambda, CloudWatch, and many others—provided they are included in the latest HIPAA-eligible services list available in AWS Artifact.

It’s critical to understand that HIPAA compliance on AWS is a shared responsibility. AWS provides a secure infrastructure foundation, aligning with frameworks like FedRAMP and NIST SP 800-53 to meet regulatory benchmarks. However, the responsibility for implementing encryption, access controls, audit logging, and secure application logic lies with the customer. Proper configuration, data segregation, and continuous monitoring are essential to ensuring your application meets HIPAA’s technical and administrative requirements.

Architecture Overview

We’ll explore the architecture layer-by-layer:

Infrastructure as Code (IaC)
Networking & Isolation
Storage (RDS, S3)
Compute (ECS, Lambda)
Messaging (SQS, SNS)
Security (IAM, KMS, Secrets Management)
Monitoring & Auditing (CloudTrail, CloudWatch)
Application Layer
DevOps & Compliance Automation

Key Components of a HIPAA-Compliant AWS Architecture

Building a HIPAA-compliant architecture on AWS involves addressing several critical components to ensure the confidentiality, integrity, and availability of PHI. Below are the key areas to focus on:

Infrastructure as Code (IaC)

Automating infrastructure through code allows you to manage environments consistently and with traceable change history. AWS-native tools like CloudFormation, or open-source alternatives like Terraform, are essential for HIPAA environments, where reproducibility and documentation are key.

Key practices:

Define all cloud resources (VPCs, subnets, IAM roles, security groups) in code
Use Git for version control and pull requests for change reviews
Integrate IaC into your CI/CD workflows
Implement tagging policies to identify PHI-related resources
Use variables or parameter files to maintain isolation between dev, test, and production

IaC also supports automated validation and compliance scans, helping ensure no manual misconfigurations compromise security.

Networking & Isolation

A secure network perimeter is foundational for protecting healthcare workloads. AWS Virtual Private Cloud (VPC) allows segmentation between public-facing and internal components. Use subnet isolation to ensure that PHI-processing services never have direct internet access.

Key components:

ALBs in public subnets route HTTPS traffic to backend services in private subnets
VPC Endpoints allow secure, private communication with AWS services like S3 and DynamoDB
Security Groups limit inbound and outbound traffic at the instance level
Network ACLs apply stateless rules to subnet traffic
VPC Flow Logs track traffic for monitoring and intrusion detection

For hybrid cloud or on-premise integrations, AWS Direct Connect and Site-to-Site VPN provide encrypted communication paths that support compliance.

Compute (ECS, Lambda)

AWS offers flexible compute models for various use cases. Containers (ECS/Fargate) and serverless functions (Lambda) are both HIPAA-eligible and suited to different workloads.

ECS/Fargate:

Run containerized services in managed clusters without managing infrastructure
Use task-level IAM roles for least-privilege access
Deploy services in private subnets and scale via auto-scaling groups
Store container logs in CloudWatch and scan images using ECR scanning

Lambda:

Ideal for background jobs and event-driven workflows (e.g., webhook processing, notifications)
Lambda functions operate in isolated runtimes with automatic scaling
Use KMS-encrypted environment variables and store secrets in AWS Secrets Manager
Log function execution via CloudWatch Logs and use CloudWatch Metrics for performance alerts

Both ECS and Lambda support robust CI/CD integration, and workloads should be continuously monitored for anomalies or unauthorized access.

Storage (RDS, S3)

Handling PHI means that data must be protected in transit and at rest. AWS offers HIPAA-eligible storage services that are scalable and secure.

Amazon RDS (Aurora, PostgreSQL, MySQL):

Use Multi-AZ deployments for failover
Enable encryption at rest via KMS
Enforce SSL/TLS connections for clients
Automate backups with retention and versioning
Enable activity streams for audit logging

Amazon S3:

Use S3 buckets with block public access settings enabled
Apply bucket policies to enforce access via VPC or IAM roles
Enable SSE-KMS encryption and configure lifecycle policies for archival to Glacier
Serve user-facing files through pre-signed URLs or CloudFront signed URLs
Enable logging of data events and access through CloudTrail

PHI data should never be accessible from public buckets, and all data transfers should be HTTPS-only.

Messaging (SQS, SNS)

Messaging layers help decouple systems and handle asynchronous workloads such as file processing, notifications, or lab result updates.

SQS:

Queue tasks for asynchronous processing (e.g., image rendering, report generation)
Encrypt messages using SSE-KMS
Use dead-letter queues (DLQ) for retry logic
Control access via IAM policies and VPC Endpoints

SNS:

Notify users or services of events (e.g., new test results)
Support fan-out to multiple consumers (SQS, Lambda)
Use topic-level encryption
Avoid sending PHI in raw message bodies; use references instead

These services ensure resilience and throughput while adhering to privacy controls.

Security Controls

Security is enforced at every layer through identity, access management, and encryption.

IAM:

Define granular policies using least privilege
Separate user, admin, and service roles
Enforce MFA for all privileged users

KMS:

Create customer-managed keys with rotation policies
Scope key usage to specific services and identities
Enable logging for every encrypt/decrypt operation

Secrets Management:

Store secrets (e.g., DB credentials, API keys) in AWS Secrets Manager or SSM Parameter Store
Enable automatic rotation for secrets
Grant read access only to the services that need them

Security misconfigurations are a common cause of data breaches—automation and continuous review help prevent them.

Monitoring & Auditing

HIPAA mandates robust logging and incident detection capabilities.

CloudTrail:

Enable across all AWS accounts and regions
Log all API activity including resource creation, updates, and deletions
Store logs in encrypted S3 buckets with lifecycle policies

CloudWatch:

Collect system and application logs
Set alarms for critical metrics like CPU spikes, memory usage, and error rates
Use Insights and dashboards for centralized visibility

AWS Config:

Track configuration drift and enforce security baselines
Alert on policy violations (e.g., public S3 bucket)

Security Hub & GuardDuty:

Detect threats, unauthorized access, or suspicious patterns
Aggregate findings into centralized dashboards
Integrate with EventBridge for automated remediation

All monitoring components should retain logs for at least 6 years to align with HIPAA’s audit requirements.

Application Layer

The application code and API surface must also enforce security.

Key strategies:

Use established web frameworks with built-in protections (e.g., OWASP Top 10)
Validate and sanitize all inputs
Use JWTs issued by Amazon Cognito or third-party IDPs
Enforce role-based access control (RBAC) and tenant isolation
Avoid logging PHI, and mask sensitive fields when required

Microservices should use encrypted service-to-service communication and operate with scoped roles.

DevOps & Continuous Compliance

A compliant system is one that can adapt securely. CI/CD pipelines can embed compliance checks, security scans, and manual approvals.

Best practices:

Use deployment pipelines with staging and production separation
Integrate static code analysis and dependency scanning
Use IAM roles for build servers and deploy agents
Require manual approval for production rollouts
Automate rollback on failure or policy violations

Periodic architecture reviews, pen tests, and disaster recovery drills ensure ongoing compliance.

Best Practices for HIPAA-Compliant AWS Architecture

To ensure a robust and compliant architecture, follow these best practices:

Area	Best Practices	Relevant AWS Services
SSL & TLS Certificates	Use SSL/TLS for encrypting data in transit; manage certificates securely.	AWS Certificate Manager
Server Management	Use managed services to reduce infrastructure management burden.	AWS Fargate, Amazon EKS, Amazon ECS
Database Management	Enable backups and use read-only follower databases to restrict PHI access.	Amazon RDS
Cloud Storage	Restrict S3 bucket access; use expiring URLs for secure data sharing.	Amazon S3, Amazon S3 Glacier
Network Configuration	Use VPCs with subnets and separate environments for isolation.	Amazon VPC, AWS Transit Gateway
Access Control	Implement least privilege access for PHI management.	AWS IAM
Monitoring	Monitor performance, optimize resources, and set up alerts for security events.	Amazon CloudWatch, Amazon SNS
Logging and Auditing	Log API calls and configuration changes for auditing and incident identification.	AWS CloudTrail, AWS Config
CI/CD	Automate deployments to avoid human error in PHI-handling applications.	AWS CodePipeline, AWS CodeCommit, AWS CodeDeploy

Use HIPAA-Eligible Services Only: Always verify that the AWS services used for PHI are listed in the AWS HIPAA Eligible Services Reference. For example, Amazon S3 can be used for secure storage, while Amazon RDS supports encrypted databases.
Automate Compliance: Use tools like AWS Service Catalog to standardize HIPAA-compliant configurations and reduce the risk of misconfigurations.
Continuous Integration/Continuous Deployment (CI/CD): Avoid manual deployments to minimize errors. Use AWS CodePipeline, CodeCommit, and CodeDeploy for automated, compliant deployments.
Secure Logging: Store logs in Amazon S3 with encryption and restrict access to ensure audit logs are secure and tamper-proof.
Multi-AZ Deployments: Deploy applications across multiple Availability Zones to ensure high availability and resilience, as recommended by Dash Solutions.
Regular Testing: Perform vulnerability scanning, penetration testing, and breach simulations to validate the effectiveness of security controls, as suggested by Christopher Adamson on Medium.

Ongoing Compliance and Monitoring

HIPAA compliance is not a one-time effort but requires continuous monitoring and verification. Key steps include:

Regular Risk Assessments: Conduct at least annual risk assessments to identify and mitigate threats to PHI.
Auditing: Use AWS CloudTrail and AWS Config to maintain audit trails and ensure compliance with HIPAA standards.
Breach Simulations: Test incident response procedures to validate your ability to detect and respond to security incidents.
Compliance Tools: Consider third-party tools like Dash ComplyOps or Exabeam for automated compliance monitoring, as noted in Exabeam’s HIPAA Guide.

AWS Shared Responsibility Model

Under the AWS Shared Responsibility Model, AWS is responsible for securing the cloud infrastructure, while customers are responsible for securing their data and configurations within the cloud. This means you must properly configure HIPAA-eligible services, implement access controls, and maintain compliance documentation. Signing the BAA does not automatically make your architecture HIPAA-compliant; it requires diligent setup and ongoing management.

Tools and Resources

AWS Documentation: The AWS HIPAA Compliance page provides detailed guidance on compliance requirements and eligible services.
Conformance Packs: Use AWS Config Conformance Packs to align with HIPAA security controls.
Third-Party Guides: Resources like Flatirons’ HIPAA Guide and TechMagic’s Compliance Checklist offer practical steps for implementation.
Partner Solutions: Engage with AWS Healthcare Competency Partners like Simform for expert guidance, as highlighted in Simform’s Blog.

Conclusion

Architecting a HIPAA-compliant cloud architecture on AWS for health applications requires a deep understanding of HIPAA regulations, AWS services, and security best practices. By leveraging HIPAA-eligible services, implementing robust encryption, access controls, and monitoring, and maintaining ongoing compliance efforts, healthcare organizations can build secure and scalable applications. AWS provides powerful tools like IAM, KMS, VPC, and CloudTrail to support these efforts, but the responsibility for proper configuration and compliance lies with the customer. With careful planning and adherence to best practices, AWS can be a trusted platform for delivering secure, compliant healthcare solutions.

Ready to Build a HIPAA-Compliant AWS Architecture?

At F3 Software, we specialize in helping healthcare companies design, build, and scale secure, compliant cloud infrastructure on AWS. Whether you’re launching a new digital health platform or need to validate an existing architecture, our team of experienced engineers will guide you every step of the way.

Here’s how we can help:

Architect HIPAA-compliant AWS environments tailored to your app’s needs
Implement best practices for encryption, access control, and monitoring
Automate infrastructure with Terraform or CloudFormation
Integrate DevOps workflows that support compliance and speed
Perform cloud security audits and prepare for HIPAA assessments

Let’s make sure your AWS environment is secure, scalable, and audit-ready.
Schedule a consultation with F3 Software and take the next step toward delivering a cloud-native, compliant healthcare solution.

👉 Contact Us to Get Started

Frequently Asked Question

Which AWS services are HIPAA-eligible?

AWS services covered under the Business Associate Addendum (BAA) include Amazon RDS, S3, ECS, Lambda, CloudWatch, IAM, Cognito, and more.

How do I encrypt PHI data on AWS?

Use AWS KMS to manage encryption keys and enable encryption for S3, RDS, EBS, and messaging services. Enforce TLS 1.2+ for all network traffic.

Is Amazon Cognito HIPAA-compliant?

Yes, Amazon Cognito is HIPAA-eligible and can be used for secure user authentication with support for MFA and identity federation.

Do I need a Business Associate Agreement (BAA) with AWS?

Yes. Before storing or processing PHI, you must sign a BAA with AWS and use only HIPAA-eligible services.

What are the best practices for HIPAA logging and auditing on AWS?

Enable AWS CloudTrail, CloudWatch Logs, Config, and Security Hub for continuous monitoring, logging, and incident response.

Can I use AWS Lambda to process PHI?

Yes, AWS Lambda is HIPAA-eligible. Just ensure encryption, access control, and audit logging are properly configured.

How should I handle backups in a HIPAA-compliant environment?

Use Amazon RDS automated backups, AWS Backup for managed policies, and encrypt all snapshots using KMS. Retain backups according to HIPAA data retention guidelines.

How do I set up a secure VPC for HIPAA workloads?

Use public and private subnets, route sensitive services through ALBs, enable VPC flow logs, and restrict access with IAM and security groups.

What’s the role of DevOps in HIPAA compliance on AWS?

DevOps enables continuous compliance by automating security checks, infrastructure deployments, vulnerability scanning, and log analysis.