The 1999 Commonwealth of Independent States Cup was the seventh edition of the competition between the champions of former republics of Soviet Union.

It was won by Spartak Moscow for the fourth time.

Starting with this edition of the tournament, all participating nations were split into two divisions.

Eight nations which were represented in 1998 Cup quarterfinals were included in the Top Division, while the other seven nations included in the First Division.

The change was implemented to reduce the number of non-competitive games between opponents with big strength gap, such as 1998 match between Spartak Moscow and Vakhsh Qurghonteppa, which was won by the Russian side with a record-setting score 19–0.