Second leg matches take place on 12th November except where marked. (31.10.08)
Results were as follows (aet - after extra time, pso - penalty shoot out, teams qualifying in bold): See reports
| Villarreal Guille Franco |
1-1 | Poli Ejido Jorge Molina |
| Real Madrid Raúl (3), Bueno |
4-3 | Real Unión Abasolo, Salcedo, Eneko Romo |
| Barcelona Messi |
1-0 | Benidorm |
| Atlético Madrid | Orihuela | |
| Valencia Angulo, Michel, Pablo Hernández |
3-0 | Portugalete |
| Sevilla Luis Fabiano (3), Maresca |
4-0 | Ponferradina |
| Deportivo Pablo Alvarez (Pen), Omar Bravo |
2-0 | Elche |
| Racing Santander Tchité, Pereira |
2-0 | Murcia |
| Espanyol Jarque, Renan (OG), Valdo |
3-0 | Celta |
| Almería José Ortíz (2), Corona |
3-0 | Rayo Vallecano |
| Valladolid Víctor, Mendunjanin |
2-2 | Hércules Gerardo, Sendoa |
| Betis Emaná, Sergio García |
2-0 | Castellón |
| Recreativo Akalé, Ersen Martin |
2-1 | Athletic Bilbao Llorente (Pen) |
| Osasuna Pandiani |
1-0 | Getafe |
| Sporting Gijón Barral (2) |
2-0 | Numancia |
| Mallorca David Navarro, Keita |
2-0 | Málaga |