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| 1st(1st leg) | ÍBV Vestmannaeyjar | - | KF Tiranë | 1:0 (1:0) | ||
| 2nd (2nd leg) | KF Tiranë | - | ÍBV Vestmannaeyjar | 1:2 (0:2) | ||
| 1st(1st leg): 13/07/1999 19:00 | 2nd (2nd leg): 21/07/1999 16:30 | Winner: ÍBV Vestmannaeyjar | ||||
| 1st(1st leg) | PFC Litex Lovech | - | Glentoran FC | 3:0 (2:0) | ||
| 2nd (2nd leg) | Glentoran FC | - | PFC Litex Lovech | 0:2 (0:0) | ||
| 1st(1st leg): 14/07/1999 16:30 | 2nd (2nd leg): 21/07/1999 19:30 | Winner: PFC Litex Lovech | ||||
| 1st(1st leg) | FK Zalgiris | - | Tsement Ararat | 2:0 (1:0) | ||
| 2nd (2nd leg) | Tsement Ararat | - | FK Zalgiris | 0:3 (0:2) | ||
| 1st(1st leg): 14/07/1999 16:30 | 2nd (2nd leg): 21/07/1999 14:00 | Winner: FK Zalgiris | ||||
| 1st(1st leg) | Partizan | - | FC Flora | 6:0 (3:0) | ||
| 2nd (2nd leg) | FC Flora | - | Partizan | 1:4 (0:2) | ||
| 1st(1st leg): 14/07/1999 18:30 | 2nd (2nd leg): 21/07/1999 17:00 | Winner: Partizan | ||||
| 1st(1st leg) | Jeunesse Esch | - | Skonto FC | 0:2 (0:0) | ||
| 2nd (2nd leg) | Skonto FC | - | Jeunesse Esch | 8:0 (2:0) | ||
| 1st(1st leg): 14/07/1999 18:30 | 2nd (2nd leg): 21/07/1999 16:30 | Winner: Skonto FC | ||||
| 1st(1st leg) | HB Tórshavn | - | Haka Valkeakoski | 1:1 (0:0) | ||
| 2nd (2nd leg) | Haka Valkeakoski | - | HB Tórshavn | 6:0 (2:0) | ||
| 1st(1st leg): 14/07/1999 19:00 | 2nd (2nd leg): 21/07/1999 17:00 | Winner: Haka Valkeakoski | ||||
| 1st(1st leg) | FK Sloga Jugomagnat | - | FK Kapaz Gäncä | 1:0 (0:0) | ||
| 2nd (2nd leg) | FK Kapaz Gäncä | - | FK Sloga Jugomagnat | 2:1 (1:1) | ||
| 1st(1st leg): 14/07/1999 19:00 | 2nd (2nd leg): 21/07/1999 15:00 | Winner: FK Sloga Jugomagnat | ||||
| 1st(1st leg) | Barry Town FC | - | Valletta FC | 0:0 (0:0) | ||
| 2nd (2nd leg) | Valletta FC | - | Barry Town FC | 3:2 (2:1) | ||
| 1st(1st leg): 14/07/1999 19:30 | 2nd (2nd leg): 21/07/1999 19:00 | Winner: Valletta FC | ||||
| 1st(1st leg) | St Patrick's Athletic | - | FC Zimbru | 0:5 (0:3) | ||
| 2nd (2nd leg) | FC Zimbru | - | St Patrick's Athletic | 5:0 (3:0) | ||
| 1st(1st leg): 14/07/1999 19:45 | 2nd (2nd leg): 21/07/1999 16:00 | Winner: FC Zimbru | ||||
