| Rank | Team | Pts. | Yellow cards | Second yellow cards | Straight red cards |
|---|---|---|---|---|---|
| 1 | Energie Cottbus | 87 | 74 | 1 | 2 |
| 2 | Arminia Bielefeld | 93 | 90 | 1 | 0 |
| 3 | SV Wehen Wiesbaden | 97 | 87 | 0 | 2 |
| 3 | FC Ingolstadt | 97 | 92 | 0 | 1 |
| 5 | Erzgebirge Aue | 104 | 93 | 2 | 1 |
| 5 | Dynamo Dresden | 104 | 93 | 2 | 1 |
| 5 | SC Verl | 104 | 87 | 4 | 1 |
| 8 | Viktoria Köln | 106 | 80 | 2 | 4 |
| 9 | 1. FC Saarbrücken | 108 | 102 | 2 | 0 |
| 10 | SpVgg Unterhaching | 112 | 95 | 4 | 1 |
| 11 | Rot-Weiss Essen | 115 | 96 | 3 | 2 |
| 11 | Borussia Dortmund II | 115 | 104 | 2 | 1 |
| 13 | SV Sandhausen | 120 | 96 | 3 | 3 |
| 14 | Waldhof Mannheim | 123 | 114 | 3 | 0 |
| 15 | Hansa Rostock | 124 | 107 | 4 | 1 |
| 15 | TSV 1860 München | 124 | 101 | 1 | 4 |
| 17 | VfL Osnabrück | 125 | 101 | 3 | 3 |
| 18 | Alemannia Aachen | 126 | 103 | 1 | 4 |
| 19 | VfB Stuttgart | 135 | 113 | 4 | 2 |
| 20 | Hannover 96 II | 138 | 116 | 4 | 2 |