HAPI FHIR is a complete implementation of the HL7 FHIR standard for healthcare interoperability in Java. Prior to version 6.9.0, when setting headers in HTTP requests, the internal HTTP client sends headers first to the host in the initial URL but also, if asked to follow redirects and a 30X HTTP response code is returned, to the host mentioned in URL in the Location: response header value. Sending the same set of headers to subsequent hosts is a problem as this header often contains privacy sensitive information or data that could allow others to impersonate the client's request. This issue has been patched in release 6.9.0. No known workarounds are available.

HL7 (Health Level 7) FHIR Core Libraries before 5.6.92 allow attackers to extract files into arbitrary directories via directory traversal from a crafted ZIP or TGZ archive (for a prepackaged terminology cache, NPM package, or comparison archive).

Users of the HAPI FHIR Testpage Overlay 5.0.0 and below can use a specially crafted URL to exploit an XSS vulnerability in this module, allowing arbitrary JavaScript to be executed in the user's browser. The impact of this vulnerability is believed to be low, as this module is intended for testing and not believed to be widely used for any production purposes.

JPA Server in HAPI FHIR before 5.4.0 allows a user to deny service (e.g., disable access to the database after the attack stops) via history requests. This occurs because of a SELECT COUNT statement that requires a full index scan, with an accompanying large amount of server resources if there are many simultaneous history requests.