One of two hidden system files that made up Microsoft's MS-DOS. The other was IO.SYS. These two system files were loaded into memory when the computer was booted. They processed the instructions in CONFIG.SYS, then loaded COMMAND.COM and finally processed the instructions in AUTOEXEC.BAT. The PC-DOS counterparts of these system files were IBMBIO.COM and IBMDOS.COM. From Executable to Text In Windows 95/98, MSDOS.SYS was changed to a text configuration file rather than an executable program. It determined among other things whether the computer booted into DOS or Windows. IO.SYS was still a binary executable.