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| Kick-off time | Match | Match Id. |
Results after: | |||
| CET | Local | 90 Min. | Extra Time | Half Time | ||
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Saturday, July 3, 1999 |
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| 15:00 | 18:00 | FC Ararat (ARM) – K. St.-Truidense VV (BEL) | M | 0 - 2 | 0 - 2 | |
| 16:00 | 19:00 | FC Karabakh Agdam (AZE) – Montpellier Hérault SC (FRA) | L | 0 - 3 | 0 - 3 | |
| 17:00 | 18:00 | FK Ventspils (LAT) – Kocaelispor Kulübü (TUR) | K | 1 - 1 | 0 - 0 | |
| 17:30 | 17:30 | MSK Zilina (SVK) – FC Metz (FRA) | H | 2 - 1 | 2 - 0 | |
| 18:00 | 18:00 | FC Cementarnica 55 (MKD) – Rostselmash Rostov-on-Don (RUS) | D | 1 - 1 | 1 - 1 | |
| 18:00 | 18:00 | SK Brann (NOR) – NK Varteks (CRO) | E | 3 - 0 | 1 - 0 | |
| 19:30 | 19:30 | Neuchâtel Xamax (SWI) – Vasas Budapest (HUN) | N | 0 - 2 | 0 - 2 | |
| 20:00 | 20:00 | KSC Lokeren (BEL) – IA Akranes (ISL) | G | 3 - 1 | 1 - 0 | |
| 20:45 | 20:45 | AC Perugia (ITA) – FC Pobeda (MKD) | A | 1 - 0 | 0 - 0 | |
| Sunday, July 4,1999 | ||||||
| 14:00 | 14:00 | FC Kobenhavn (DEN) – KP Polonia Warszawa (POL) | I | 0 - 3 | 0 - 0 | |
| 17:00 | 18:00 | FC Jokerit (FIN) – Floriana FC (MLT) | O | 2 - 1 | 1 - 0 | |
| 17:00 | 18:00 | FC Ceahlaul Piatra Neamt (ROM) – NK Jedinstvo (BHZ) | P | 2 - 1 | 0 - 1 | |
| 17:30 | 17:30 | FC Basel (SWI) – FC Boby-Sport Brno (CZE) | C | 0 - 0 | 0 - 0 | |
| 18:00 | 18:00 | MSV Duisburg (GER) – Newry Town FC (NIR) | B | 2 - 0 | 0 - 0 | |
| 18:00 | 18:00 | NK Rudar Velenje (SLO) – SC Austria Lustenau (AUT) | F | 1 - 2 | 0 - 2 | |
| 18:00 | 18:00 | Hammarby IF (SWE) – FC Gomel (BLS) | J | 4 - 0 | 1 - 0 | |
| FC Metz (France) took the vacant place of ESP2 | ||||||
CET = Central European Time
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