A branch auditing system can be automatically injected into a computer program, in one embodiment, in response to a programming call provided in source code by a programmer who has selected a particular branch, in a set of possible branches, for auditing. The branch auditing system can record, in an obfuscated data structure, a path taken at the particular branch and the parameters associated with the branch and later an auditor can determine whether the path taken was valid, and if the path taken was invalid, operations can be performed to protect the program, system and/or user.