Up until verion 5.0 PC DOS and MS-DOS had same exact features and utilities, but IBM's PC DOS 6, which was officially introduced as PC DOS 6.1 in June of 1993, is somewhat different than Microsoft's MS-DOS 6.0. All the fundamental DOS commands are the same, but PC DOS 6.1 includes direct support for pen-based computing and the PC Card. Also, PC-DOS 6.1 includes an enhanced text editor with split screens and macros, a program scheduler, an antivirus monitor, a more comprehensive backup utility that includes tape and backup scheduling, and a full-screen Undelete for both DOS and Windows that lets you preview your files before you delete them. QBasic was dropped and PC DOS 6.1 had no built- in programming language.

For the first time, PC-DOS became available from IBM as a retail product, not just for IBM systems.

PC DOS 6.1 had quite a number of small bugs, which were corrected in PC-DOS 6.3 in April 1994.