Obsidian has become one of the most popular note-taking and knowledge-management tools for professionals who value flexibility and privacy. Its local-first design, markdown files, and extensive plugin ecosystem make it a favorite among researchers, therapists, and consultants. However, when it comes to handling protected health information (PHI) under the Health Insurance Portability and Accountability Act (HIPAA), using Obsidian can introduce serious compliance challenges. This article explains the key risks and what healthcare providers should consider before storing PHI in Obsidian.
1. Obsidian Is Not Officially HIPAA-Compliant
As of 2025, Obsidian does not advertise HIPAA compliance and does not provide a Business Associate Agreement (BAA) — a mandatory contract under HIPAA when a service provider handles PHI on behalf of a covered entity. Without a BAA, any healthcare organization or business associate using Obsidian Sync or Obsidian Publish to store or transmit PHI would be in violation of HIPAA.
Obsidian’s official documentation emphasizes that users maintain full control of their data, and compliance responsibility lies entirely with the end user (Obsidian Help Center). This means the company does not make any commitments to safeguard PHI under U.S. healthcare privacy laws.
2. Local Storage Reduces but Does Not Eliminate Risk
One of Obsidian’s selling points is its local-first model — your vaults are stored as markdown files on your own device, not on Obsidian’s servers. This setup can seem appealing for privacy-conscious users. However, HIPAA compliance requires much more than local storage.
Even locally stored PHI must still meet HIPAA’s technical, administrative, and physical safeguards. This includes encryption, device-level access control, audit logs, user authentication, and secure data backup. If PHI is kept on a local drive without full-disk encryption or password protection, a lost or stolen device could still result in a reportable HIPAA breach.
3. Obsidian Sync and Publish Add Cloud-Based Exposure
Many users rely on Obsidian Sync for cross-device access and Obsidian Publish for sharing notes online. While convenient, both services rely on Obsidian’s cloud infrastructure — and neither is designed for HIPAA-regulated data.
According to Obsidian’s Sync documentation, data is end-to-end encrypted in transit and at rest. However, HIPAA requires more than encryption — it requires signed BAAs, formal risk assessments, access audits, and breach notification procedures. Since Obsidian does not provide a BAA, using Sync or Publish for PHI would still violate HIPAA, even if the data is technically encrypted.
4. Plugin Ecosystem Increases Security Complexity
Obsidian’s extensibility is one of its greatest strengths — but also a significant risk factor for compliance. Thousands of third-party plugins can access, modify, or export your notes. Unless each plugin is thoroughly vetted, it could potentially expose sensitive PHI through unintended data syncs, logs, or API calls.
HIPAA requires that all software components interacting with PHI be properly secured and monitored. Because Obsidian’s plugin ecosystem is open and community-maintained, there’s no standardized security review process. A single untrusted plugin could compromise an otherwise secure vault.
5. Lack of Audit Trails and Access Logs
Under HIPAA’s Security Rule, covered entities must maintain detailed audit trails of data access, modifications, and deletions. Obsidian does not provide built-in audit logging or administrative monitoring tools. While version-control plugins can track file changes, they do not meet HIPAA’s requirements for tamper-resistant audit logs with user attribution.
This makes it impossible to prove compliance or detect unauthorized access events — both of which are essential for HIPAA investigations and risk assessments.
6. Legal and Regulatory Liability
Even if you use Obsidian locally and apply best security practices, you are still fully responsible for compliance. In the event of a data breach, healthcare regulators may view the lack of a BAA and insufficient safeguards as willful neglect. Penalties can range from $100 to $50,000 per violation, depending on the severity and intent.
Moreover, using unapproved software for PHI can violate organizational IT and compliance policies, leading to internal disciplinary or contractual penalties in addition to regulatory ones.
7. HIPAA-Compliant Alternatives and Mitigation Steps
If you work with patient information, you should avoid using Obsidian for PHI unless your organization’s compliance officer explicitly approves it under strict local-only controls. Consider the following alternatives and precautions:
- Use tools that sign BAAs. Platforms such as Microsoft OneNote (Enterprise), Google Workspace (Enterprise), and Notion Enterprise can sign BAAs for eligible business accounts.
- Encrypt your local vaults. Use full-disk encryption and strong passwords to protect data stored on your device.
- Disable cloud sync for PHI. Keep any patient-related vaults fully offline and disconnected from Obsidian Sync or Publish.
- Vet plugins carefully. Avoid third-party plugins that transmit or back up data externally.
- Document compliance decisions. Maintain written records of risk assessments and justify why a local-only vault is considered acceptable (if ever used for PHI).
Conclusion
Obsidian’s flexibility and privacy-friendly design make it an excellent tool for general personal knowledge management, research, and writing. However, it is not HIPAA compliant and should not be used to store or share protected health information in professional healthcare contexts.
Without a BAA, audit logs, or controlled plugin architecture, Obsidian cannot meet the administrative and technical safeguards required by HIPAA. For healthcare providers and therapists, the safest approach is to use a purpose-built, HIPAA-compliant platform — or an offline, air-gapped solution with encryption and documented access control policies.
Looking for a secure offline knowledge manager built for compliance-sensitive professionals? Explore VaultBook — an encrypted, offline-first alternative designed for HIPAA-conscious users.