| 2. Round | 24/01/2009 | Cruz Azul | - | Atlas Guadalajara | 4:0 |  |
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| 3. Round | 01/02/2009 | Atlas Guadalajara | - | UANL Tigres | 1:1 | ||||
| 4. Round | 07/02/2009 | Club San Luis | - | Atlas Guadalajara | 2:1 | |
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| 5. Round | 15/02/2009 | Atlas Guadalajara | - | Atlante | 1:0 | |
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| 8. Round | 01/03/2009 | Puebla FC | - | Atlas Guadalajara | 1:1 | ||||
| 11. Round | 22/03/2009 | Atlas Guadalajara | - | UAG Tecos | 0:0 | ||||
| 14. Round | 19/04/2009 | Santos Laguna | - | Atlas Guadalajara | 4:1 | ||||
| 16. Round | 03/05/2009 | Monarcas Morelia | - | Atlas Guadalajara | 4:2 |
Mexico