The Second Division is geographically divided into 5 zones: West (Northwestern European Russia), Centre (Northern and Eastern European Russia), South (Southern European Russia), Ural-Povolzhye (Southern Urals and Western Siberia), and East (Rest of Siberia). The number of clubs in each zone varies between years. In 2006, there are 81 clubs in the division (there were 79 in 2005).

The winners of each zone are automatically promoted into the First Division. The bottom finishers of each zone lose professional status and are relegated into the Amateur Football League.