SaaS HIPAA Compliance: Everything You Need To Know

Healthcare organizations have fully embraced SaaS.

Collaboration tools, analytics platforms, scheduling software - it is all in the cloud.

But here’s the problem: most SaaS stacks are not built with HIPAA in mind, and many teams are using tools that silently put Protected Health Information (PHI) at risk.

What is HIPAA compliance for SaaS?

HIPAA (Health Insurance Portability and Accountability Act) is the U.S. law that protects patient data.

Any SaaS platform that stores, transmits, or processes PHI must meet HIPAA requirements.

For SaaS apps, that typically means:

  • Data encryption in transit and at rest
  • Access controls and audit logs
  • Business Associate Agreements (BAAs) in place
  • Breach notification protocols
  • Physical and network safeguards

Why SaaS complicates HIPAA compliance

Most healthcare IT teams assume their cloud vendors are compliant.

But that’s not always true, especially when:

  • Teams adopt apps without IT approval (shadow IT)
  • Free versions are used without security features
  • BAAs are not signed or not stored centrally
  • Access controls are not enforced or reviewed

Suddenly, PHI is sitting in Slack, Google Drive, or some AI-powered app that marketing just started using.

And no one realized it.

Here is a quick visual to explain the risk tiers when considering a tool handling PHI:

What Are the Most Common HIPAA Violations?

HIPAA violations often start with small oversights that snowball into major compliance risks.

Here are the most frequent mistakes healthcare organizations make when using SaaS:

1. No Business Associate Agreement
Using a SaaS tool that handles PHI without a signed BAA is one of the most common violations.

Without a BAA in place, you are not HIPAA compliant, no matter how secure the tool claims to be.

2. Unauthorized access to PHI
Employees accessing patient records they don’t need or ex-employees who still have login access both create major privacy and compliance risks.

3. Failure to encrypt data
If PHI is not encrypted in transit or at rest, and a breach occurs, the penalties are severe.

Encryption is a baseline expectation under HIPAA.

4. Improper disposal of PHI
Old patient data left in unused cloud tools or deactivated accounts must be securely deleted.

Simply abandoning accounts is not compliant.

5. Use of unapproved SaaS apps
Shadow IT is a major HIPAA risk.

When teams sign up for apps without IT review, PHI can end up in systems with no safeguards or visibility.

How to make SaaS HIPAA Compliant

Compliance does not mean ditching SaaS.

It means knowing what’s in use, locking it down, and staying proactive.

Here is how:

  1. Inventory your SaaS stack – Know every tool in use, across every department.
  2. Categorize apps by risk – Is PHI involved? Is there a signed BAA?
  3. Centralize access management – Use SSO, provisioning, and off-boarding workflows.
  4. Standardize usage – Limit sensitive workflows to approved tools.
  5. Audit regularlyLogs, access, and tool sprawl should all be reviewed.

How Perimeters.io automates HIPAA Compliance

Perimeters gives you total visibility into your SaaS stack, including apps IT didn’t know existed.

From there, it helps you:

• Automatically detect and remediate HIPAA compliance gaps (plus 11 other frameworks)
• Flag apps without compliance certificates
• Enforce least privilege access and remove dormant accounts
• Automate app usage audits and compliance checks
• Lock down shadow IT before it creates exposure

With Perimeters, HIPAA compliance becomes manageable, even in a modern SaaS first environment.

Book a demo to see how Perimeters helps you become HIPAA compliant in just 5 minutes per day.

Frequently Asked Questions

Can software be HIPAA compliant?

Software itself cannot be HIPAA compliant out of the box.

Compliance depends on how it’s configured, used, and secured within your organization.

However, a SaaS provider can support HIPAA compliance by offering required safeguards (like encryption and access controls) and signing a Business Associate Agreement.

Do I need a BAA to be HIPAA compliant?

Yes. If a SaaS provider handles Protected Health Information on your behalf, you must have a signed Business Associate Agreement in place to be HIPAA compliant.

Without a BAA, using the service for PHI, even if it is secure, violates HIPAA.

What is the best platform for HIPAA compliance?

The best platform for HIPAA compliance depends on your needs, but for SaaS oversight and misconfigurations, Perimeters.io stands out.

It gives you full visibility into your cloud app stack, flags tools without compliance certificates, automates access control, and helps you enforce HIPAA policies at scale, even across shadow IT.

Ready To Automatically Secure Your SaaS?

Book a live demo and see how.