| Tourney Name: | UEFA Intertoto Cup |
| Year: | 1999 |
| Dates: | 19 June – 24 August 1999 |
| Num Teams: | 60[1] |
| Champion Other: |  JuventusWest Ham United  Montpellier |
| Matches: | 114 |
| Goals: | 300 |
| Prevseason: | 1998 |
| Nextseason: | 2000 |
The 1999 UEFA Intertoto Cup finals were won by Montpellier, Juventus, and West Ham United. All three teams advanced to the UEFA Cup.
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Ventspils won 2–1 on aggregate.----Sint-Truiden won 8–1 on aggregate.----Polonia Warsaw won 4–0 on aggregate.----4–4 on aggregate. Pobeda won 4–3 on penalties.----2–2 on aggregate, Rudar Velenje won on away goals rule.----MŠK Žilina won 4–0 on aggregate.----Ararat Yerevan won 2–0 on aggregate.----Varteks won 4–3 on aggregate.----Vasas won 7–1 on aggregate.----Neuchâtel Xamax won 2–0 on aggregate.----Ceahlăul Piatra Neamţ won 2–0 on aggregate.----1–1 on aggregate, Gomel won 3–1 on penalties.----Newry Town won 2–1 on aggregate.----2–2 on aggregate, Qarabağ won on away goals rule.----Cementarnica 55 won 8–2 on aggregate.----Basel won 6–0 on aggregate.----Jedinstvo Bihać won 3–1 on aggregate.----Floriana won 4–3 on aggregate.----ÍA won 6–3 on aggregate.----Jokerit won 7–1 on aggregate.
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Perugia won 1–0 on aggregate.----Duisburg won 2–1 on aggregate.----Basel won 4–2 on aggregate.----Rostselmash won 3–2 on aggregate.----3–3 on aggregate; Varteks won 5–4 on penalties----Austria Lustenau won 4–2 on aggregate.----Lokeren won 6–2 on aggregate.----Metz won 4–2 on aggregate.----Polonia Warsaw won 4–1 on aggregate.----Hammarby won 6–2 on aggregate.----Kocaelispor won 3–1 on aggregate.----Kocaelispor won 9–0 on aggregate.----Sint-Truiden won 5–1 on aggregate.----Vasas won 3–0 on aggregate.----Jokerit won 3–0 on aggregate.----Ceahlăul Piatra Neamţ won 5–2 on aggregate.
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Montpellier won 4–1 on aggregate.----1–1 on aggregate, Juventus won on away goals rule.----The game was abandoned in the 114th minute of extra time due to some objects being thrown on the pitch, some even hitting the referee. UEFA banned Perugia and awarded a 3–0 win to Trabzonspor.
Trabzonspor won 4–2 on aggregate.---- West Ham United won 2–1 on aggregate.----Heerenveen won 4–0 on aggregate.---- 2–2 on aggregate, Rennes won on away goals rule.----3–3 on aggregate, Hamburg won on away goals rule.----Austria Wien won 3–2 on aggregate.----2–2 on aggregate, Rostselmash won on away goals rule.----Duisburg won 3–0 on aggregate.----2–2 on aggregate, Metz won on away goals rule.----Polonia Warsaw won 4–1 on aggregate.
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Montpellier won 3–1 on aggregate.----Hamburger SV won 6–3 on aggregate.----Juventus won 9–1 on aggregate.----Rennes won 4–2 on aggregate.----West Ham United won 2–0 on aggregate.----Metz won 6–2 on aggregate.
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2–2 on aggregate; Montpellier won 3–0 on penalties----West Ham United won 3–2 on aggregate.----Juventus won 4–2 on aggregate.