A boot sector virus is one that infects by replacing code in the boot sector of a floppy disk (and sometimes a hard disk) with its own code. This ensures that whenever an attempt is made to boot from the infected disk, the virus loads before the operating system.

These viruses are very uncommon now, but in the first half of the 1990s, when floppy disks were the main means of transferring data, they represented the main threat to PC users. Typically, a boot sector virus infected the hard disk when a user inadvertently left an infected floppy disk in drive A. When the PC was next booted, the system would try to boot from the floppy disk and the virus code would execute, regardless of whether or not the floppy disk was a system disk or just a data disk. Most boot sector viruses then infected the MBR [Master Boot Record] of the hard disk, rather than the boot sector.