Abstract: A method and apparatus for implementing a BIOS-level floppy boot-sector virus prevention system. A floppy boot protection system installed on a computer system queries a user to indicate whether or not the computer system is to be booted from a floppy disk inserted in a floppy disk drive of the computer system prior to booting from the floppy disk. If the user responds in the affirmative, the computer system is booted from the floppy disk and operation proceeds as usual. If the user responds in the negative, the floppy disk boot is skipped, the user is advised of this fact, and the computer system attempts to boot from the next device listed in its boot table. In one aspect, during setup of the computer system, the user is able to enable or disable the floppy boot protection system as desired. If the user fails to respond to the query within a predetermined amount of time, the boot protection system defaults to skipping the floppy disk boot and proceeding as described above.