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The flaw hypothesis methodology is a technique used to predict and analyze flaws in software systems. It involves compiling a list of potential flaws based on a system’s documentation and specifications.
DEFINITION:
System analysis and penetration technique in which the specification and documentation for an information system are analyzed to produce a list of hypothetical flaws. This list is prioritized on the basis of the estimated probability that a flaw exists, on the ease of exploiting it, and on the extent of control or compromise it would provide. The prioritized list is used to perform penetration testing of a system.
SOURCE: CNSSI-4009

A “Flaw Hypothesis Methodology” example might include the following. A penetration tester analyzes a web application by first thoroughly reviewing its design and code to identify potential vulnerabilities. Next, he may forming specific hypotheses about where flaws might exist (like insecure input validation or improper session management). Finally, he may try testing those hypothesized flaws to see if they can be exploited. This is essentially “guessing” where vulnerabilities might be based, then verifying them through testing. This process is often used in security assessments to proactively identify potential security risks in a system.
Key steps in a Flaw Hypothesis Methodology
If a vulnerability is found, the tester tries to identify other similar vulnerabilities in the system based on the same underlying flaw, expanding the scope of the testing.
See NIST Testing Documentation