Vulnerabilities in pkg:pypi/biopython

PACKAGE
Advisory Identifier: GHSA-x3vf-39hj-gxr4
Share
Advisory Summary

CVE-2025-68463 is a MODERATE (CVSS 4.9) biopython is vulnerable to doctype vulnerability (CWE-611: Improper Restriction of XML External Entity Reference) affecting Biopython libraries in the PyPI ecosystem. The issue involves biopython is vulnerable to doctype xml external entity (xxe) injection through bio.entrez. Remediation is available in the latest vendor maintenance releases.

1 Known Advisory Record(s)
Package Vulnerability Intelligence

pkg:pypi/biopython

1 Known Advisory Record(s)

Vulnerability advisories affecting package pkg:pypi/biopython. Select an advisory below to view technical details or fixes.

Advisory ID CVE / NVD Severity Summary
GHSA-x3vf-39hj-gxr4 CVE-2025-68463 MODERATE Biopython is vulnerable to doctype XML external entity (XXE) injection through Bio.Entrez

CVE-2025-68463 at a Glance

CVE Identifier CVE-2025-68463
GHSA Identifier GHSA-x3vf-39hj-gxr4
Severity MODERATE
CVSS v3.1 Base Score 4.9
CWE Classification CWE-611: Improper Restriction of XML External Entity Reference
Affected Product Biopython
Package Ecosystem PyPI
Published Date
Last Updated

Security Impact

CVSS: 4.9

The security impact metrics below are parsed directly from the CVSS v3.1 vector string (CVSS:3.1/AV:N/AC:H/PR:L/UI:N/S:C/C:L/I:N/A:L).

Attack Vector Network (AV:N)
Attack Complexity High (AC:H)
Privileges Required Low (PR:L)
User Interaction None (UI:N)
Scope Changed (S:C)
Confidentiality Low (C:L)
Integrity None (I:N)
Availability Low (A:L)

How to Fix CVE-2025-68463

To remediate this vulnerability, upgrade all affected Biopython dependencies to a patched release. Both direct and transitive dependencies should be checked, as frameworks or security libraries may pull in vulnerable versions transitively.

biopython fixed: Latest secure release 
pip install biopython>=Latest secure release
Verify Direct and Transitive Dependencies

Run the following command in your project directory to verify that all resolved dependencies use the patched release: 

pip show biopython

How to Check if You Are Affected

To determine whether your Python environment is affected by CVE-2025-68463, inspect your installed packages using pip:

pip show biopython

Analyze the terminal output to locate any version of Biopython in your dependency tree. If any resolved version matches the vulnerable ranges listed in the table below (for example, versions earlier than the patched release), your application is affected.

Note: The pip show biopython command checks currently installed packages in your active Python environment.

Technical Details

Vulnerability Mechanism & Technical Analysis

This vulnerability is classified under CWE-611: Improper Restriction of XML External Entity Reference, where the product processes an xml document that can contain xml entities with uris that resolve to documents outside of the intended sphere of control, causing the product to embed incorrect documents into its output. In Biopython, software state validation or input boundaries are circumvented during processing. Review the official source advisory statement below for specific affected components, classes, and reproduction details.

Source Advisory Statement

Bio.Entrez in Biopython through 1.86 allows doctype XXE.

CVE-2025-68463 Affected Biopython Versions

1 component(s)
Product / Package Ecosystem Affected Versions Fixed Version
biopython
pypi/biopython
PyPI
≤ 1.86

References

NVD — CVE-2025-68463 NVD
https://nvd.nist.gov/vuln/detail/CVE-2025-68463
Biopython Source Repository REPOSITORY
https://github.com/biopython/biopython/issues/5109
Security Fix Commit FIX COMMIT
https://github.com/biopython/biopython/commit/736c96f37b190732ecca9da80ad0cb9d4967214d
Biopython Source Repository REPOSITORY
https://github.com/biopython/biopython
Biopython Source Repository REPOSITORY
https://github.com/biopython/biopython/blob/master/NEWS.rst
pypi.org/project/biopython/1... WEB
https://pypi.org/project/biopython/1.87
Biopython Security Information SECURITY
http://www.openwall.com/lists/oss-security/2026/05/08/16

Frequently Asked Questions

What is CVE-2025-68463?
CVE-2025-68463 is a security vulnerability in Biopython involving Biopython is vulnerable to doctype XML external entity (XXE) injection through Bio.Entrez under CWE-611: Improper Restriction of XML External Entity Reference.
Which Biopython versions are affected?
Affected versions include releases prior to current release patches across affected packages: biopython.
What version fixes CVE-2025-68463?
Upgrading to current release patches (or the latest patched release for your respective branch) resolves the vulnerability.
Is biopython affected?
Yes, biopython is affected in releases prior to Latest secure release. Upgrade your dependency to Latest secure release or later.
What is the CVSS score of CVE-2025-68463?
CVE-2025-68463 has a CVSS v3.1 base score of 4.9 (MODERATE) with vector string CVSS:3.1/AV:N/AC:H/PR:L/UI:N/S:C/C:L/I:N/A:L.
What CWE is associated with CVE-2025-68463?
CVE-2025-68463 is classified under CWE-611: Improper Restriction of XML External Entity Reference (The product processes an XML document that can contain XML entities with URIs that resolve to documents outside of the intended sphere of control, causing the product to embed incorrect documents into its output.).
How can I check PyPI dependencies for CVE-2025-68463?
Run the dependency tree command: 'pip show biopython'. This command lists direct and transitive dependencies in your build configuration so you can verify if a vulnerable version is resolved.
Machine-readable OSV JSON OSV v1.5 Schema
Normalized schema output
View Raw JSON 
{
  "schema_version" : "1.4.0",
  "id" : "GHSA-x3vf-39hj-gxr4",
  "modified" : "2026-05-12T13:37:18Z",
  "published" : "2025-12-18T06:30:13Z",
  "aliases" : [ "CVE-2025-68463" ],
  "summary" : "Biopython is vulnerable to doctype XML external entity (XXE) injection through Bio.Entrez",
  "details" : "Bio.Entrez in Biopython through 1.86 allows doctype XXE.",
  "severity" : [ {
    "type" : "CVSS_V3",
    "score" : "CVSS:3.1/AV:N/AC:H/PR:L/UI:N/S:C/C:L/I:N/A:L"
  } ],
  "affected" : [ {
    "package" : {
      "ecosystem" : "PyPI",
      "name" : "biopython"
    },
    "ranges" : [ {
      "type" : "ECOSYSTEM",
      "events" : [ {
        "introduced" : "0"
      }, {
        "last_affected" : "1.86"
      } ]
    } ]
  } ],
  "references" : [ {
    "type" : "ADVISORY",
    "url" : "https://nvd.nist.gov/vuln/detail/CVE-2025-68463"
  }, {
    "type" : "WEB",
    "url" : "https://github.com/biopython/biopython/issues/5109"
  }, {
    "type" : "WEB",
    "url" : "https://github.com/biopython/biopython/commit/736c96f37b190732ecca9da80ad0cb9d4967214d"
  }, {
    "type" : "WEB",
    "url" : "https://github.com/biopython/biopython"
  }, {
    "type" : "WEB",
    "url" : "https://github.com/biopython/biopython/blob/master/NEWS.rst"
  }, {
    "type" : "WEB",
    "url" : "https://pypi.org/project/biopython/1.87"
  }, {
    "type" : "WEB",
    "url" : "http://www.openwall.com/lists/oss-security/2026/05/08/16"
  } ],
  "database_specific" : {
    "cwe_ids" : [ "CWE-611" ],
    "severity" : "MODERATE",
    "github_reviewed" : true,
    "github_reviewed_at" : "2025-12-18T22:16:29Z",
    "nvd_published_at" : "2025-12-18T06:15:50Z"
  }
}