Disclosed herein are methods, systems, and computer-readable storage media for annotation driven integrity program verification. The method includes distributing verification calls configured to verify a function across call paths leading to the function in source code, generating a binary from the source code having placeholders associated with the verification calls, and filling each placeholder in the binary with verification data or reference checksums. Alternatively, the method includes receiving source code having a verification call, replacing the verification call with one or more equivalent verification calls distributed over a call path, replacing each verification call with a checksum function generating placeholders while compiling, generating a binary based on the placeholders, and filling each placeholder in the binary with reference checksums. The system includes a processor and a module controlling the processor to perform the methods. The computer-readable storage medium includes instructions for controlling a computer to perform the methods.