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| 1st(1st leg) | Real Unión | - | Real Valladolid | 1:1 (1:1) | ||
| 2nd (2nd leg) | Real Valladolid | - | Real Unión | 0:1 (0:1) | ||
| 1st(1st leg): 09/11/1999 19:30 | 2nd (2nd leg): 01/12/1999 19:45 | Winner: Real Unión | ||||
| 1st(1st leg) | UD Alzira | - | Málaga CF | 0:0 (0:0) | ||
| 2nd (2nd leg) | Málaga CF | - | UD Alzira | 2:0 (0:0) | ||
| 1st(1st leg): 09/11/1999 20:00 | 2nd (2nd leg): 01/12/1999 20:00 | Winner: Málaga CF | ||||
| 1st(1st leg) | Club Bermeo | - | Real Betis | 0:0 (0:0) | ||
| 2nd (2nd leg) | Real Betis | - | Club Bermeo | 2:0 (2:0) | ||
| 1st(1st leg): 10/11/1999 19:15 | 2nd (2nd leg): 01/12/1999 20:00 | Winner: Real Betis | ||||
| 1st(1st leg) | Barakaldo CF | - | CE Premià | 1:0 (0:0) | ||
| 2nd (2nd leg) | CE Premià | - | Barakaldo CF | 2:2 (0:0) | ||
| 1st(1st leg): 10/11/1999 19:15 | 2nd (2nd leg): 01/12/1999 19:30 | Winner: Barakaldo CF | ||||
| 1st(1st leg) | CA Osasuna | - | Sevilla FC | 1:0 (1:0) | ||
| 2nd (2nd leg) | Sevilla FC | - | CA Osasuna | 1:1 (1:1) | ||
| 1st(1st leg): 10/11/1999 19:30 | 2nd (2nd leg): 01/12/1999 20:00 | Winner: CA Osasuna | ||||
| 1st(1st leg) | CD Logroñés | - | Real Sociedad | 2:1 (0:1) | ||
| 2nd (2nd leg) | Real Sociedad | - | CD Logroñés | 0:1 (0:0) | ||
| 1st(1st leg): 10/11/1999 19:30 | 2nd (2nd leg): 01/12/1999 19:15 | Winner: CD Logroñés | ||||
| 1st(1st leg) | SD Compostela | - | CD Numancia | 4:2 (1:1) | ||
| 2nd (2nd leg) | CD Numancia | - | SD Compostela | 3:2 (0:1) | ||
| 1st(1st leg): 10/11/1999 19:30 | 2nd (2nd leg): 01/12/1999 19:30 | Winner: SD Compostela | ||||
| 1st(1st leg) | SD Ponferradina | - | Albacete | 1:1 (0:1) | ||
| 2nd (2nd leg) | Albacete | - | SD Ponferradina | 3:1 (0:1, 1:1) aet | ||
| 1st(1st leg): 10/11/1999 19:30 | 2nd (2nd leg): 01/12/1999 20:00 | Winner: Albacete | ||||
| 1st(1st leg) | CD Ourense | - | Getafe CF | 1:0 (0:0) | ||
| 2nd (2nd leg) | Getafe CF | - | CD Ourense | 1:2 (1:1) | ||
| 1st(1st leg): 10/11/1999 19:30 | 2nd (2nd leg): 01/12/1999 19:30 | Winner: CD Ourense | ||||
| 1st(1st leg) | Gimnástica Segoviana | - | Sporting Gijón | 0:0 (0:0) | ||
| 2nd (2nd leg) | Sporting Gijón | - | Gimnástica Segoviana | 2:1 (0:0) | ||
| 1st(1st leg): 10/11/1999 19:30 | 2nd (2nd leg): 01/12/1999 19:30 | Winner: Sporting Gijón | ||||
| 1st(1st leg) | SD Eibar | - | CD Toledo | 1:0 (1:0) | ||
| 2nd (2nd leg) | CD Toledo | - | SD Eibar | 0:0 (0:0) | ||
| 1st(1st leg): 10/11/1999 19:30 | 2nd (2nd leg): 01/12/1999 20:00 | Winner: SD Eibar | ||||
| 1st(1st leg) | UD Salamanca | - | Rayo Vallecano | 2:2 (1:1) | ||
| 2nd (2nd leg) | Rayo Vallecano | - | UD Salamanca | 4:2 (1:0) | ||
| 1st(1st leg): 10/11/1999 19:45 | 2nd (2nd leg): 01/12/1999 20:00 | Winner: Rayo Vallecano | ||||
| 1st(1st leg) | Novelda CF | - | CP Almería | 0:1 (0:1) | ||
| 2nd (2nd leg) | CP Almería | - | Novelda CF | 0:0 (0:0) | ||
| 1st(1st leg): 10/11/1999 19:45 | 2nd (2nd leg): 01/12/1999 20:15 | Winner: CP Almería | ||||
| 1st(1st leg) | Talavera CF | - | CP Mérida | 1:0 (1:0) | ||
| 2nd (2nd leg) | CP Mérida | - | Talavera CF | 3:0 (0:0) | ||
| 1st(1st leg): 10/11/1999 19:45 | 2nd (2nd leg): 01/12/1999 20:00 | Winner: CP Mérida | ||||
| 1st(1st leg) | Recreativo Huelva | - | Real Zaragoza | 0:0 (0:0) | ||
| 2nd (2nd leg) | Real Zaragoza | - | Recreativo Huelva | 4:0 (1:0) | ||
| 1st(1st leg): 10/11/1999 20:00 | 2nd (2nd leg): 01/12/1999 19:30 | Winner: Real Zaragoza | ||||
| 1st(1st leg) | CF Extremadura | - | CD Alavés | 1:1 (0:1) | ||
| 2nd (2nd leg) | CD Alavés | - | CF Extremadura | 1:0 (0:0) | ||
| 1st(1st leg): 10/11/1999 20:00 | 2nd (2nd leg): 01/12/1999 19:30 | Winner: CD Alavés | ||||
| 1st(1st leg) | UD Melilla | - | Athletic Club | 2:2 (1:1) | ||
| 2nd (2nd leg) | Athletic Club | - | UD Melilla | 3:2 (0:1) | ||
| 1st(1st leg): 10/11/1999 20:00 | 2nd (2nd leg): 01/12/1999 19:15 | Winner: Athletic Club | ||||
| 1st(1st leg) | Coria CF | - | UE Lleida | 2:4 (0:3) | ||
| 2nd (2nd leg) | UE Lleida | - | Coria CF | 1:1 (1:1) | ||
| 1st(1st leg): 10/11/1999 20:00 | 2nd (2nd leg): 01/12/1999 19:30 | Winner: UE Lleida | ||||
| 1st(1st leg) | Villarreal CF | - | CD Leganés | 0:1 (0:0) | ||
| 2nd (2nd leg) | CD Leganés | - | Villarreal CF | 0:3 (0:0, 0:1) aet | ||
| 1st(1st leg): 10/11/1999 20:00 | 2nd (2nd leg): 01/12/1999 20:00 | Winner: Villarreal CF | ||||
| 1st(1st leg) | Badajoz CF | - | UD Las Palmas | 1:1 (0:1) | ||
| 2nd (2nd leg) | UD Las Palmas | - | Badajoz CF | 1:0 (0:0) | ||
| 1st(1st leg): 10/11/1999 20:00 | 2nd (2nd leg): 30/11/1999 21:00 | Winner: UD Las Palmas | ||||
| 1st(1st leg) | Zamora CF | - | CD Tenerife | 2:2 (2:2) | ||
| 2nd (2nd leg) | CD Tenerife | - | Zamora CF | 4:0 (4:0) | ||
| 1st(1st leg): 10/11/1999 20:00 | 2nd (2nd leg): 01/12/1999 21:00 | Winner: CD Tenerife | ||||
| 1st(1st leg) | Córdoba CF | - | Espanyol Barcelona | 1:1 (0:0) | ||
| 2nd (2nd leg) | Espanyol Barcelona | - | Córdoba CF | 2:0 (2:0) | ||
| 1st(1st leg): 10/11/1999 20:15 | 2nd (2nd leg): 01/12/1999 19:30 | Winner: Espanyol Barcelona | ||||
| 1st(1st leg) | Hércules CF | - | Racing Santander | 0:0 (0:0) | ||
| 2nd (2nd leg) | Racing Santander | - | Hércules CF | 3:0 (3:0) | ||
| 1st(1st leg): 10/11/1999 20:15 | 2nd (2nd leg): 01/12/1999 19:00 | Winner: Racing Santander | ||||
| 1st(1st leg) | Lorca CF | - | Real Oviedo | 0:1 (0:0) | ||
| 2nd (2nd leg) | Real Oviedo | - | Lorca CF | 2:0 (2:0) | ||
| 1st(1st leg): 10/11/1999 20:30 | 2nd (2nd leg): 01/12/1999 19:30 | Winner: Real Oviedo | ||||
