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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 10, 1999 |
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| 16:00 | 15:00 | Newry Town FC (NIR) – MSV Duisburg (GER) | B | 1 - 0 | 1 - 0 | |
| 16:00 | 16:00 | KP Polonia Warszawa (POL) – FC Kobenhavn (DEN) | I |
1 - 1
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1 - 0 | |
| 17:00 | 19:00 | Rostselmash Rostov-on-Don (RUS) – FC Cementarnica 55 (MKD) | D | 2 - 1 | 1 - 0 | |
| 17:00 | 17:00 | Floriana FC (MLT) – FC Jokerit (FIN) | O | 1 - 1 | 1 - 0 | |
| 18:00 | 18:00 | NK Jedinstvo (BHZ) – FC Ceahlaul Piatra Neamt (ROM) | P | 1 - 3 | 1 - 3 | |
| 19:00 | 19:00 | SC Austria Lustenau (AUT) – NK Rudar Velenje (SLO) | F | 2 - 1 | 1 - 1 | |
| 20:00 | 20:00 | Vasas Budapest (HUN) – Neuchâtel Xamax (SWI) | N | 1 - 0 | 1 - 0 | |
| 20:00 | 20:00 | NK Varteks (CRO) – SK Brann (NOR) | E | 3 - 0 | 3 - 0* | 2 - 0 |
| *NK Varteks won 5 - 4 on penalty kicks | ||||||
| 20:00 | 20:00 | K. St.-Truidense VV (BEL) – FC Ararat (ARM) | M | 3 - 1 | 2 - 0 | |
| 20:00 | 20:00 | Montpellier Hérault SC (FRA) – FC Karabakh Agdam (AZE) | L | 6 - 0 | 2 - 0 | |
| Sunday, July 11,1999 | ||||||
| 17:00 | 18:00 | FC Gomel (BLS) – Hammarby IF (SWE) | J | 2 - 2 | 0 - 1 | |
| 17:00 | 18:00 | Kocaelispor Kulübü (TUR) – FK Ventspils (LAT) | K | 2 - 0 | 1 - 0 | |
| 17:30 | 17:30 | FC Pobeda (MKD) – AC Perugia (ITA) | A | 0 - 0 | 0 - 0 | |
| 18:00 | 16:00 | IA Akranes (ISL) – KSC Lokeren (BEL) | G | 1 - 3 | 1 - 1 | |
| 18:00 | 18:00 | FC Boby-Sport Brno (CZE) – FC Basel (SWI) | C | 2 - 4 | 1 - 2 | |
| 18:00 | 18:00 | FC Metz (FRA) – MSK Zilina (SVK) | H | 3 - 0 | 0 - 0 | |
| underlined teams in 3rd round | ||||||
| NOTE: FC Metz (France) took the vacant place of ESP2 | ||||||
CET = Central European Time
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