Amkar and Kuban won the promotion on the dramatic final day of the season, leaving Terek and Tom in the First Division.
The following clubs have earned promotion by winning tournaments in their respective zones: In a newly introduced Russian Super Cup Lokomotiv overcame CSKA 4–3 on penalties after the match ended 1–1.
CSKA Moscow were unsuccessful in the 2003–04 UEFA Champions League, as they lost in the second qualifying round to FK Vardar 2–3 on aggregate.
Lokomotiv were level on points with Inter but qualified for the knock-out rounds thanks to a 3–0 home win and away draw.
Spartak Moscow knocked out Esbjerg fB and Dinamo București in the first two rounds and qualified for the spring phase of the competition.