VulnerabilityPublished 18 Mar 2026

CVE-2026-31971: samtools htslib · Stack-based Buffer Overflow

Affects samtools htslibSource CVE Database V5

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Not known to be exploited · CVSS 7.1 High : upgrade to 1.22.2 or 1.21.1 soon.

Data as of 30 Oct 2026, 06:59 UTC

CVSS 4.0 base score

7.1High

How severe the flaw is on the 0–10 CVSS scale.

EPSS: 0.3% chance of exploitation in 30 days – higher than 28% of CVEsExploit Prediction Scoring System: the likelihood attackers will use this flaw soon.
Patch: Available – fixed in 1.22.2, 1.21.1

CVSS:4.0/AV:N/AC:L/AT:N/PR:N/UI:P/VC:N/VI:H/VA:L/SC:N/SI:N/SA:N

Attack Vector: Network
Attack Complexity: Low
Attack Requirements: None
Privileges Required: None
User Interaction: Passive
Vulnerable system confidentiality: None
Vulnerable system integrity: High
Vulnerable system availability: Low
Subsequent system confidentiality: None
Subsequent system integrity: None
Subsequent system availability: None

Bold values are the worst case: easiest to exploit or largest impact.

Attack Vector: Network: The vulnerable system is bound to the network stack and the set of possible attackers extends beyond the other options listed below, up to and including the entire Internet. Such a vulnerability is often termed “remotely exploitable” and can be thought of as an attack being exploitable at the protocol level one or more network hops away (e.g., across one or more routers).
Attack Complexity: Low: The attacker must take no measurable action to exploit the vulnerability. The attack requires no target-specific circumvention to exploit the vulnerability. An attacker can expect repeatable success against the vulnerable system.
Attack Requirements: None: The successful attack does not depend on the deployment and execution conditions of the vulnerable system. The attacker can expect to be able to reach the vulnerability and execute the exploit under all or most instances of the vulnerability.
Privileges Required: None: The attacker is unauthorized prior to attack, and therefore does not require any access to settings or files of the vulnerable system to carry out an attack.
User Interaction: Passive: Successful exploitation of this vulnerability requires limited interaction by the targeted user with the vulnerable system and the attacker’s payload. These interactions would be considered involuntary and do not require that the user actively subvert protections built into the vulnerable system.
Vulnerable system confidentiality: None: There is no loss of confidentiality within the Vulnerable System.
Vulnerable system integrity: High: There is a total loss of integrity, or a complete loss of protection. For example, the attacker is able to modify any/all files protected by the vulnerable system. Alternatively, only some files can be modified, but malicious modification would present a direct, serious consequence to the vulnerable system.
Vulnerable system availability: Low: Performance is reduced or there are interruptions in resource availability. Even if repeated exploitation of the vulnerability is possible, the attacker does not have the ability to completely deny service to legitimate users. The resources in the Vulnerable System are either partially available all of the time, or fully available only some of the time, but overall there is no direct, serious consequence to the Vulnerable System.
Subsequent system confidentiality: None: There is no loss of confidentiality within the Subsequent System or all confidentiality impact is constrained to the Vulnerable System.
Subsequent system integrity: None: There is no loss of integrity within the Subsequent System or all integrity impact is constrained to the Vulnerable System.
Subsequent system availability: None: There is no impact to availability within the Subsequent System or all availability impact is constrained to the Vulnerable System.

Definitions: FIRST CVSS v4.0 specification.

Exploitation evidence

Disclosed: evidence found.
CVE published 18 Mar 2026
Detectable: no evidence on record.
No public nuclei template indexed
Weaponized: no evidence on record.
No public exploit code indexed in Metasploit or Exploit-DB
Exploited in the wildExploited: no evidence on record.
Not in CISA KEV and no source reports exploitation
Observed by OffSeq MirageSeen by Mirage: no evidence on record.
No attack traffic recorded by OffSeq Mirage sensors

A missing step is not evidence of safety. Sources: cve.org (opens in a new tab), the Metasploit, Exploit-DB and nuclei-templates index as of 29 Oct 2026.

Disclosed: The CVE record is public on cve.org. Its publication is t = 0.
Detectable: A public nuclei template can find exposed instances, for defenders and attackers alike.
Weaponized: A Metasploit exploit module or Exploit-DB entry exists (Metasploit scanner modules do not count), or CISA SSVC or the CVSS exploit maturity reports a public proof of concept.
Exploited in the wild: CISA KEV lists it, CISA SSVC rates exploitation active, or a source reports attacks.
Observed by OffSeq Mirage: OffSeq Mirage honeypot sensors recorded attack traffic for this CVE, or found exposed hosts without attack traffic.

Moments are spaced evenly, not to scale; a dashed line marks a gap of six months or more. Deltas count from t = 0. Sources that give only a date (CISA KEV, Exploit-DB, or a time of exactly 00:00Z) read “same day” rather than hours. Metasploit modules carry the flaw’s disclosure date, not their release date, and nuclei templates carry no date, so both appear above but not on the timeline.

What to do

Upgrade htslib to 1.22.2 or 1.21.1; samtools/htslib to 1.21.1.

Affected software

Product	Affected	Fixed in
samtoolshtslib	Affected <1.21.1 >=1.22 <1.22.2 =1.23	Fixed in 1.22.2 1.21.1
GitHubsamtools/htslib`pkg:github/samtools/htslib`Other threats	Affected <1.21.1 =1.23	Fixed in 1.21.1

Check your own hosts for these packages with threat-finder (opens in a new tab), our free open-source scanner.

AI-suggested

To mitigate CVE-2026-31971, organizations should immediately upgrade all instances of htslib to versions 1.21.1, 1.22.2, 1.23.1, or later, where the vulnerability has been fixed. Since no workaround exists, patching is the primary defense. Additionally, implement strict file validation and scanning policies to detect and block malicious or malformed CRAM files before processing. Restrict access to bioinformatics processing environments to trusted users and networks to reduce the risk of opening crafted files. Employ application whitelisting and sandboxing techniques to limit the impact of potential exploitation. Monitoring and logging of bioinformatics tool usage can help detect anomalous behavior indicative of exploitation attempts. Educate users about the risks of opening untrusted genomic data files. For environments where immediate patching is not feasible, consider isolating vulnerable systems and limiting network exposure to reduce attack surface. Finally, maintain up-to-date backups of critical data to enable recovery in case of compromise.

Description

HTSlib is a library for reading and writing bioinformatics file formats. CRAM is a compressed format which stores DNA sequence alignment data using a variety of encodings and compression methods. When reading data encoded using the `BYTE_ARRAY_LEN` method, the `cram_byte_array_len_decode()` failed to validate that the amount of data being unpacked matched the size of the output buffer where it was to be stored. Depending on the data series being read, this could result either in a heap or a stack overflow with attacker-controlled bytes. Depending on the data stream this could result either in a heap buffer overflow or a stack overflow. If a user opens a file crafted to exploit this issue it could lead to the program crashing, overwriting of data structures on the heap or stack in ways not expected by the program, or changing the control flow of the program. It may be possible to use this to obtain arbitrary code execution. Versions 1.23.1, 1.22.2 and 1.21.1 include fixes for this issue. There is no workaround for this issue.

Impact

The impact of CVE-2026-31971 is significant for organizations handling genomic data, particularly those using samtools or other bioinformatics tools relying on htslib. Exploitation can lead to denial of service through program crashes or, more severely, arbitrary code execution, which may allow attackers to execute malicious payloads on affected systems. This could result in unauthorized access to sensitive genomic data, manipulation or corruption of research data, disruption of critical bioinformatics workflows, and potential compromise of broader IT infrastructure if the exploited system is part of a larger network. Given the specialized nature of the software, the threat primarily targets research labs, healthcare organizations, pharmaceutical companies, and government agencies involved in genomics. The ability to execute code remotely without authentication but requiring user interaction (opening a crafted file) increases the risk in environments where untrusted files might be processed. The lack of a workaround means that vulnerable systems remain exposed until patched, increasing the window of opportunity for attackers once exploit techniques become publicly available.

CWE-121Stack-based Buffer Overflow (opens in a new tab)
Variant weaknessLikelihood of exploit: HighCWE Top 25 (2025): #14
The product writes past the end of a buffer that was allocated on the stack.
Operation · Build and Compilation · Environment Hardening
Use automatic buffer overflow detection mechanisms that are offered by certain compilers or compiler extensions. Examples include: the Microsoft Visual Studio /GS flag, Fedora/Red Hat FORTIFY_SOURCE GCC flag, StackGuard, and ProPolice, which provide various mechanisms including canary-based detection and range/index…
Architecture and Design
Use an abstraction library to abstract away risky APIs. Not a complete solution.
Implementation
Implement and perform bounds checking on input.
OWASP Cheat Sheets
XML Security (opens in a new tab)
Mass Assignment (opens in a new tab)
OWASP ASVS 4.0.3
V13.3.1 (opens in a new tab)
V5.1.4 (opens in a new tab)
V5.1.3 (opens in a new tab)
From MITRE CWE, MITRE CAPEC and OWASP (Top 10, OpenCRE).
CWE-122Heap-based Buffer Overflow (opens in a new tab)
Variant weaknessLikelihood of exploit: HighCWE Top 25 (2025): #16
The product writes past the end of a buffer that was allocated on the heap.
Pre-design: Use a language or compiler that performs automatic bounds checking.
Architecture and Design
Use an abstraction library to abstract away risky APIs. Not a complete solution.
Operation · Build and Compilation · Environment Hardening
Use automatic buffer overflow detection mechanisms that are offered by certain compilers or compiler extensions. Examples include: the Microsoft Visual Studio /GS flag, Fedora/Red Hat FORTIFY_SOURCE GCC flag, StackGuard, and ProPolice, which provide various mechanisms including canary-based detection and range/index…
OWASP Cheat Sheets
XML Security (opens in a new tab)
Mass Assignment (opens in a new tab)
OWASP ASVS 4.0.3
V13.3.1 (opens in a new tab)
V5.1.4 (opens in a new tab)
V5.1.3 (opens in a new tab)
Attack patterns
Forced Integer Overflow (opens in a new tab)
From MITRE CWE, MITRE CAPEC and OWASP (Top 10, OpenCRE).
CWE-787Out-of-bounds Write (opens in a new tab)
Base weaknessLikelihood of exploit: HighCWE Top 25 (2025): #5
The product writes data past the end, or before the beginning, of the intended buffer.
Requirements · Language Selection
Use a language that does not allow this weakness to occur or provides constructs that make this weakness easier to avoid.
Architecture and Design · Libraries or Frameworks
Use a vetted library or framework that does not allow this weakness to occur or provides constructs that make this weakness easier to avoid.
Operation · Build and Compilation · Environment Hardening
Use automatic buffer overflow detection mechanisms that are offered by certain compilers or compiler extensions. Examples include: the Microsoft Visual Studio /GS flag, Fedora/Red Hat FORTIFY_SOURCE GCC flag, StackGuard, and ProPolice, which provide various mechanisms including canary-based detection and range/index…
OWASP Cheat Sheets
XML Security (opens in a new tab)
Mass Assignment (opens in a new tab)
OWASP ASVS 4.0.3
V13.3.1 (opens in a new tab)
V5.1.4 (opens in a new tab)
V5.1.3 (opens in a new tab)
From MITRE CWE, MITRE CAPEC and OWASP (Top 10, OpenCRE).
CWE-1284Improper Validation of Specified Quantity in Input (opens in a new tab)
Base weakness
The product receives input that is expected to specify a quantity (such as size or length), but it does not validate or incorrectly validates that the quantity has the required properties.
Implementation · Input Validation
Assume all input is malicious. Use an "accept known good" input validation strategy, i.e., use a list of acceptable inputs that strictly conform to specifications. Reject any input that does not strictly conform to specifications, or transform it into something that does.
OWASP Cheat Sheets
XML Security (opens in a new tab)
Mass Assignment (opens in a new tab)
OWASP ASVS 4.0.3
V13.3.1 (opens in a new tab)
V5.1.4 (opens in a new tab)
V5.1.3 (opens in a new tab)
From MITRE CWE, MITRE CAPEC and OWASP (Top 10, OpenCRE).

References

Community reviews

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Exploitation evidence

What to do

Affected software

Description

AI analysisMachine-generated, updated 18 Mar 2026, 20:12 UTC

WeaknessesCWE-121, CWE-122, CWE-787 +1

Technical details

References

Community reviews

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