The seven Bezirke in Bavaria each play their own cup competition which in turn used to function as a qualifying to the German Cup (DFB-Pokal). Since 1998 these seven cup-winners plus the losing finalist of the region that won the previous event advance to the newly introduced Bavarian Cup, the Toto-Pokal. The two finalists of this competition advance to the German Cup. Bavarian clubs which play in the first or second Bundesliga are not permitted to take part in the event, their reserve teams however can. The seven regional cup winners were qualified for the first round.
The two clubs, TSV 1860 Rosenheim and SpVgg Landshut, who qualified through the Bavarian Cup for the DFB Cup 1999-00 both were knocked out in the second round of the national cup competition, having received a bye in the first round: