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| U | Rapid Wien | - | Valletta FC | 3:0 (0:0) | ||
| R | Valletta FC | - | Rapid Wien | 0:2 (0:0) | ||
| U: 28.07.1999 16:00 | R: 04.08.1999 18:00 | Winnaars: Rapid Wien | ||||
| U | Dinamo Tbilisi | - | FC Zimbru | 2:1 (0:0) | ||
| R | FC Zimbru | - | Dinamo Tbilisi | 2:0 (1:0) | ||
| U: 28.07.1999 16:00 | R: 04.08.1999 17:00 | Winnaars: FC Zimbru | ||||
| U | Rapid Bucureşti | - | Skonto FC | 3:3 (1:2) | ||
| R | Skonto FC | - | Rapid Bucureşti | 2:1 (0:1) | ||
| U: 28.07.1999 16:30 | R: 04.08.1999 20:00 | Winnaars: Skonto FC | ||||
| U | Dnepr Mogilev | - | AIK Solna | 0:1 (0:0) | ||
| R | AIK Solna | - | Dnepr Mogilev | 2:0 (0:0) | ||
| U: 28.07.1999 17:00 | R: 04.08.1999 19:00 | Winnaars: AIK Solna | ||||
| U | Anorthosis Famagusta | - | Slovan Bratislava | 2:1 (1:0) | ||
| R | Slovan Bratislava | - | Anorthosis Famagusta | 1:1 (0:0) | ||
| U: 28.07.1999 17:30 | R: 04.08.1999 18:00 | Winnaars: Anorthosis Famagusta | ||||
| U | PFC Litex Lovech | - | Widzew Łódź | 4:1 (1:0) | ||
| R | Widzew Łódź | - | PFC Litex Lovech | 3:2 (1:1, 4:1, 4:1) d.p. | ||
| U: 28.07.1999 17:30 | R: 04.08.1999 20:15 | Winnaars: Widzew Łódź | ||||
| U | CSKA Moskou | - | Molde FK | 2:0 (1:0) | ||
| R | Molde FK | - | CSKA Moskou | 4:0 (0:0) | ||
| U: 28.07.1999 18:00 | R: 04.08.1999 18:00 | Winnaars: Molde FK | ||||
| U | Haka Valkeakoski | - | Rangers FC | 1:4 (0:3) | ||
| R | Rangers FC | - | Haka Valkeakoski | 3:0 (2:0) | ||
| U: 28.07.1999 18:00 | R: 04.08.1999 20:45 | Winnaars: Rangers FC | ||||
| U | Dinamo Kiev | - | FK Zalgiris | 2:0 (1:0) | ||
| R | FK Zalgiris | - | Dinamo Kiev | 0:1 (0:1) | ||
| U: 28.07.1999 18:00 | R: 04.08.1999 17:00 | Winnaars: Dinamo Kiev | ||||
| U | Beşiktaş | - | Hapoel Haifa | 1:1 (0:0) | ||
| R | Hapoel Haifa | - | Beşiktaş | 0:0 (0:0) | ||
| U: 28.07.1999 19:45 | R: 04.08.1999 19:30 | Winnaars: Hapoel Haifa | ||||
| U | FK Sloga Jugomagnat | - | Brøndby IF | 0:1 (0:1) | ||
| R | Brøndby IF | - | FK Sloga Jugomagnat | 1:0 (1:0) | ||
| U: 28.07.1999 20:00 | R: 04.08.1999 20:45 | Winnaars: Brøndby IF | ||||
| U | Maribor Teatanic | - | KRC Genk | 5:1 (1:1) | ||
| R | KRC Genk | - | Maribor Teatanic | 3:0 (1:0) | ||
| U: 28.07.1999 20:00 | R: 04.08.1999 20:30 | Winnaars: Maribor Teatanic | ||||
| U | Partizan | - | HNK Rijeka | 3:1 (2:0) | ||
| R | HNK Rijeka | - | Partizan | 0:3 (0:2) | ||
| U: 28.07.1999 20:15 | R: 04.08.1999 20:30 | Winnaars: Partizan | ||||
| U | ÍBV Vestmannaeyjar | - | MTK Hungaria | 0:2 (0:1) | ||
| R | MTK Hungaria | - | ÍBV Vestmannaeyjar | 3:1 (3:0) | ||
| U: 28.07.1999 21:00 | R: 04.08.1999 20:45 | Winnaars: MTK Hungaria | ||||
