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Security & Compliance 2026-02-10 7 min read

The Engineering HIPAA Compliance Checklist for Healthcare Startups

A practical engineering checklist for healthcare startups to implement HIPAA-compliant cloud architecture and pass enterprise hospital vendor security audits.

Why Most Startups Fail Hospital Vendor Audits

Building a healthcare app is the easy part. Getting a major hospital system to sign a Business Associate Agreement (BAA) and onboard your product as a vendor is a completely separate, far more grueling process.

Hospital IT security teams will send you a questionnaire with 200+ questions about your architecture. Here is what they are almost certain to ask about.

1. Encryption at Rest and In Transit

Every datastore holding Protected Health Information (PHI) must be encrypted at rest. This is not optional.

# AWS RDS with KMS encryption
resource "aws_db_instance" "phi_store" {
  storage_encrypted = true
  kms_key_id        = aws_kms_key.phi_key.arn
}

In transit, all communication must use TLS 1.2 or higher. Any API that accepts unencrypted HTTP requests will be an immediate audit failure.

2. Automated Audit Logging

You must be able to prove who accessed which PHI record and when. AWS CloudTrail plus immutable S3 log storage is the standard pattern. Logs must be retained for a minimum of 6 years per HIPAA's documentation retention rules.

3. Access Control & Zero Trust

Implement the principle of least privilege. No production IAM role should have blanket * permissions. Every microservice should have its own role with exactly the S3 buckets, DynamoDB tables, or Secrets Manager secrets it needs — nothing more.

4. Business Associate Agreements (BAAs)

Every vendor in your supply chain that could touch PHI must have a signed BAA. This includes:

  • Your cloud provider (AWS, GCP, Azure all offer BAAs)
  • Your email provider (only some providers sign BAAs)
  • Your analytics/logging tools

Conclusion

Passing a hospital vendor audit is a months-long engineering effort, not an afternoon of paperwork. Starting with a Zero Trust architecture from day one is the only cost-effective approach.

See our HIPAA & SOC 2 Cloud Architecture service for a full breakdown of our security engineering approach.

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Written by Engineering Team

HealthSyncX Interoperability Division