Abstract: A computer system which verifies the integrity of installed software on the computer system. A reserved non-DOS hard disk partition is used to store routines which pre-boot the computer system and provide a secure environment from which to verify files. Routines start by performing a self check on the non-DOS partition routines, then check the master boot record and boot sectors of the hard disk. System files of the user DOS partition are verified next and any additional designated user files are verified until the computer system is verified. Since the computer booted from an atypical partition, the drives are remapped to account for the shift in logical disk drive addressing. When completed and prior to booting from the user partition, an NVRAM latch is set to prevent unauthorized modification of the initial checksums. The non-DOS partition contains three different sets of DOS: a copy of the user DOS, if DOS is installed on the user partition; a subset of DOS and a backup of the DOS subset.