| 3. Round | 10/08/2008 | UANL Tigres | - | Atlas Guadalajara | 3:0 | ||||
| 4. Round | 17/08/2008 | Atlas Guadalajara | - | Club San Luis | 0:1 | ||||
| 5. Round | 24/08/2008 | Atlante | - | Atlas Guadalajara | 2:2 | ||||
| 6. Round | 28/08/2008 | Atlas Guadalajara | - | CF América | 1:1 | ||||
| 7. Round | 31/08/2008 | Pumas UNAM | - | Atlas Guadalajara | 3:0 | ||||
| 8. Round | 14/09/2008 | Atlas Guadalajara | - | Puebla FC | 2:0 | ||||
| 9. Round | 21/09/2008 | Indios Juárez | - | Atlas Guadalajara | 2:4 |  |
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| 10. Round | 28/09/2008 | Atlas Guadalajara | - | Deportivo Guadalajara | 0:1 | ||||
| 11. Round | 04/10/2008 | UAG Tecos | - | Atlas Guadalajara | 3:1 | ||||
| 12. Round | 12/10/2008 | Atlas Guadalajara | - | CF Monterrey | 0:0 | ||||
| 13. Round | 19/10/2008 | Club Necaxa | - | Atlas Guadalajara | 0:1 | ||||
| 14. Round | 26/10/2008 | Atlas Guadalajara | - | Santos Laguna | 2:1 | ||||
| 15. Round | 02/11/2008 | Deportivo Toluca | - | Atlas Guadalajara | 4:0 | ||||
| 16. Round | 09/11/2008 | Atlas Guadalajara | - | Monarcas Morelia | 2:1 | ||||
| 17. Round | 16/11/2008 | CF Pachuca | - | Atlas Guadalajara | 1:1 |  |
Uruguay