MSDOS.SYS an important system file on MS-DOS and Windows 9x systems. It is run after IO.SYS. In MS-DOS, it contains the core operating system code, the kernel. On Windows 9x systems, the DOS kernel code is merged into IO.SYS, and MSDOS.SYS is an ASCII file containing configuration directives.
By default, the file is located in the root directory of the bootable drive/partition (normally C:\) and has the hidden, read-only, and system file attributes set.
IBM PC-DOS and DR DOS used the file IBMDOS.COM for the same purpose.
Windows NT-based operating systems (NT 3.1-4, 2000, XP, and 2003) use the NTLDR file and NT 6+ ( Vista, 2008, and 7) uses bootmgr instead, as they have a different boot sequence.
MSDOS.SYS in Windows 9x (95/98/ME):