The 1999 Russian Second Division was the eighth edition of the Russian Second Division. There were 6 zones with 108 teams starting the competition (1 was excluded before the end of the season).
Source: RSSSF (A) Advance to a further round; (R) Relegated Notes:
^ abFC Spartak Shchyolkovo were awarded a 3-0 victory in an away game vs. FC Torpedo-2. Torpedo-2 had multiple injuries and junior national team call ups before the game and started the game with only 8 players. As two more players were injured and Torpedo-2 was left with 6 players on the field, the game was abandoned with the score 2-0 for Spartak at that time.
^FC Saturn-d Ramenskoye was admitted into the division without participating in any national-level competitions in 1998.
^FC Oazis Yartsevo promoted from the Russian Amateur Football League.
^FC Dynamo St. Petersburg renamed to FC Dynamo-SPb. They did not participate in any national-level competitions in 2000.
^ abFC Spartak-Peresvet were awarded a 3-0 victory over FC Dynamo-SPb as Dynamo-SPb did not arrive for the game.
^ abFC Torpedo-2 were awarded a 3-0 victory over FC Energiya as Energiya did not arrive for the game.
^FC Spartak Bryansk renamed to FC Spartak-Peresvet. They did not participate in any national-level competitions in 2000.
Source: RSSSF (A) Advance to a further round; (R) Relegated Notes:
^FC Lada-Togliatti-VAZ Togliatti renamed to FC Lada.
^FC Metallurg Vyksa promoted from the Amateur Football League.
^ abFC Energiya Ulyanovsk and FC Torpedo Arzamas did not participate in any national-level competitions in 2000.
^FC Dynamo-Mashinostroitel Kirov was admitted into the division without participating in any national-level competitions in 1998. They were called FC Dynamo Kirov in 1998.
^FC Neftyanik Pokhvistnevo were excluded from the league after playing 15 games and gaining 13 points. Opponents were awarded 3-0 wins in the remaining matches. Neftyanik did not participate in any national-level competitions in 2000.
^FC Reformatsiya Abakan promoted from the Amateur Football League.
^ abFC Dynamo Omsk and FC Samotlor-XXI Nizhnevartovsk moved from Zone Ural to Zone East.
^FC Samotlor-XXI Nizhnevartovsk were deducted 12 points for not paying transfer fees on time. They did not participate in any national-level competitions in 2000.