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Group A
Group B
Group C
Group D
Quarter-finals
Semi-finals
Final
2006 Main
Group A
| Pl | W | D | L | Diff | Pts | |||
| 1 | Urawa Reds | 6 | 5 | 1 | 0 | 14:5 | 9 | 16 |
| 2 | Yokohama F. Marinos | 6 | 3 | 1 | 2 | 9:8 | 1 | 10 |
| 3 | Avispa Fukuoka | 6 | 1 | 2 | 3 | 4:8 | -4 | 5 |
| 4 | FC Tokyo | 6 | 0 | 2 | 4 | 1:7 | -6 | 2 |
Group B
| Pl | W | D | L | Diff | Pts | |||
| 1 | Kawasaki Frontale | 6 | 5 | 0 | 1 | 14:8 | 6 | 15 |
| 2 | Kashima Antlers | 6 | 3 | 0 | 3 | 12:9 | 3 | 9 |
| 3 | Oita Trinita | 6 | 3 | 0 | 3 | 6:9 | -3 | 9 |
| 4 | Kyoto | 6 | 1 | 0 | 5 | 10:16 | -6 | 3 |
Group C
| Pl | W | D | L | Diff | Pts | |||
| 1 | Chiba | 6 | 4 | 1 | 1 | 10:7 | 3 | 13 |
| 2 | Shimizu S-Pulse | 6 | 2 | 2 | 2 | 8:8 | 0 | 8 |
| 3 | Albirex Niigata | 6 | 1 | 3 | 2 | 7:8 | -1 | 6 |
| 4 | Sanfrecce Hiroshima | 6 | 1 | 2 | 3 | 7:9 | -2 | 5 |
Group D
| Pl | W | D | L | Diff | Pts | |||
| 1 | Cerezo Osaka | 6 | 3 | 3 | 0 | 8:5 | 3 | 12 |
| 2 | Iwata | 6 | 3 | 1 | 2 | 10:9 | 1 | 10 |
| 3 | Kofu | 6 | 2 | 2 | 2 | 8:7 | 1 | 8 |
| 4 | Omiya Ardija | 6 | 2 | 1 | 3 | 9:10 | -1 | 7 |
| 5 | Nagoya Grampus | 6 | 0 | 3 | 3 | 6:10 | -4 | 3 |
2006 Play Offs
Quarter-finals
| 1 | Kashima Antlers | Gamba Osaka | 2 : 0, 0 : 0 |
| 2 | Iwata | Yokohama F. Marinos | 0 : 2, 1 : 2 |
| 3 | Kawasaki Frontale | Urawa Reds | 2 : 1, 3 : 4 |
| 4 | Cerezo Osaka | Chiba | 2 : 3, 2 : 5 |
Semi-finals
| 1 | Kashima Antlers | Yokohama F. Marinos | 1 : 2, 1 : 0 |
| 2 | Kawasaki Frontale | Chiba | 2 : 3, 2 : 2 |
Final
| 1 | Kashima Antlers | Chiba | 0 : 2 |
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