| 1. Round | 06/08/2006 | Atlas Guadalajara | - | Pumas UNAM | 1:0 | ||||
| 3. Round | 20/08/2006 | Atlas Guadalajara | - | CF América | 2:0 | ||||
| 7. Round | 09/09/2006 | Atlante | - | Atlas Guadalajara | 0:2 | ||||
| 8. Round | 14/09/2006 | Atlas Guadalajara | - | Veracruz (old) | 3:1 | ||||
| 10. Round | 24/09/2006 | Atlas Guadalajara | - | Deportivo Toluca | 0:0 | ||||
| 11. Round | 01/10/2006 | Santos Laguna | - | Atlas Guadalajara | 1:1 | ||||
| 12. Round | 08/10/2006 | Atlas Guadalajara | - | CF Pachuca | 1:1 | ||||
| 15. Round | 29/10/2006 | Deportivo Guadalajara | - | Atlas Guadalajara | 3:1 | ||||
| 16. Round | 05/11/2006 | Atlas Guadalajara | - | Club Necaxa | 2:1 | ||||
| 17. Round | 11/11/2006 | Gallos Blancos (old) | - | Atlas Guadalajara | 1:1 |
Mexico