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| 16.09.2006 | 07:00 | Kyoto Purple Sanga | - | FC Tokyo | 1:0 (1:0) | |
| 07:00 | Oita Trinita | - | Gamba Osaka | 0:2 (0:2) | ||
| 08:00 | Shimizu S-Pulse | - | Kashima Antlers | 1:2 (0:1) | ||
| 12:00 | Urawa Red Diamonds | - | Sanfrecce Hiroshima | 2:1 (1:1) | ||
| 12:00 | Nagoya Grampus Eight | - | Albirex Niigata | 3:1 (2:1) | ||
| 12:00 | Cerezo Osaka | - | JEF United Chiba | 3:2 (1:1) | ||
| 12:00 | Avispa Fukuoka | - | Yokohama F. Marinos | 1:3 (0:1) | ||
| 17.09.2006 | 12:00 | Kawasaki Frontale | - | Júbilo Iwata | 3:4 (1:1) | |
| 12:00 | Ventforet Kofu | - | RB Omiya Ardija | 3:2 (1:0) |
| » Clasificación | En casa | Fuera de casa | 1.ª vuelta | 2.ª vuelta | 1.ª parte | 2.ª parte |
| # | Equipo | P | V | E | D | Goles | DG | Pun. | |
|---|---|---|---|---|---|---|---|---|---|
| 1 |
|
Gamba Osaka | 23 | 16 | 4 | 3 | 58:29 | 29 | 52 |
| 2 |
|
Urawa Red Diamonds | 23 | 15 | 4 | 4 | 46:18 | 28 | 49 |
| 3 |
|
Kawasaki Frontale | 23 | 14 | 5 | 4 | 58:32 | 26 | 47 |
| 4 |
|
Shimizu S-Pulse | 23 | 14 | 2 | 7 | 42:27 | 15 | 44 |
| 5 |
|
Kashima Antlers | 23 | 13 | 3 | 7 | 39:34 | 5 | 42 |
| 6 |
|
Oita Trinita | 23 | 10 | 6 | 7 | 36:31 | 5 | 36 |
| 7 |
|
Júbilo Iwata | 23 | 9 | 7 | 7 | 45:34 | 11 | 34 |
| 8 |
|
Yokohama F. Marinos | 23 | 9 | 5 | 9 | 38:29 | 9 | 32 |
| 9 |
|
JEF United Chiba | 23 | 9 | 5 | 9 | 43:41 | 2 | 32 |
| 10 |
|
RB Omiya Ardija | 23 | 9 | 3 | 11 | 30:39 | -9 | 30 |
| 11 |
|
Nagoya Grampus Eight | 23 | 7 | 7 | 9 | 35:39 | -4 | 28 |
| 12 |
|
Ventforet Kofu | 23 | 8 | 4 | 11 | 30:47 | -17 | 28 |
| 13 |
|
FC Tokyo | 23 | 8 | 3 | 12 | 37:40 | -3 | 27 |
| 14 |
|
Albirex Niigata | 23 | 8 | 3 | 12 | 28:49 | -21 | 27 |
| 15 |
|
Sanfrecce Hiroshima | 23 | 6 | 5 | 12 | 30:42 | -12 | 23 |
| 16 |
|
Kyoto Purple Sanga | 23 | 4 | 6 | 13 | 30:53 | -23 | 18 |
| 17 |
|
Cerezo Osaka | 23 | 4 | 4 | 15 | 29:52 | -23 | 16 |
| 18 |
|
Avispa Fukuoka | 23 | 1 | 10 | 12 | 22:40 | -18 | 13 |
