The 1998–99 UEFA Cup was won by Parma in the final against Marseille. It was their second title in the competition.
It was the last edition of the old format UEFA Cup, before the Cup Winners' Cup was merged into it to include domestic cup winners, and an extra knockout round was added. The new format was last played in the 2003–04 season and was later replaced by a Group Stage format in 2004–05.
The labels in the parentheses show how each team qualified for the place of its starting round:[1]
Argeş Piteşti won 7–1 on aggregate.
CSKA Sofia won 3–1 on aggregate.
Omonia won 8–6 on aggregate.
Shakhtar Donetsk won 6–1 on aggregate.
Red Star Belgrade won 11–0 on aggregate.
Inter Bratislava won 4–0 on aggregate.
Polonia Warsaw won 5–1 on aggregate.
VPS won 4–2 on aggregate.
Kilmarnock won 2–1 on aggregate.
Mura won 8–2 on aggregate.
3–3 on aggregate; Zalgiris Vilnius won on away goals.
Hapoel Tel Aviv won 6–2 on aggregate.
Malmö won 7–0 on aggregate.
Germinal Ekeren won 4–1 on aggregate.
Rangers won 7–3 on aggregate.
Oţelul Galaţi won 4–1 on aggregate.
IFK Göteborg won 7–0 on aggregate.
Ferencváros won 14–1 on aggregate.
Anderlecht won 6–0 on aggregate.
Wisła Kraków won 7–0 on aggregate.
Red Star Belgrade won 4–2 on aggregate.
AEK Athens won 6–4 on aggregate.
Servette won 5–3 on aggregate.
4–4 on aggregate; Argeş Piteşti won on away goals.
CSKA Sofia won 2–0 on aggregate.
2–2 on aggregate; Fenerbahçe won on away goals.
Silkeborg won 2–0 on aggregate.
Rangers won 2–0 on aggregate.
Slavia Prague won 4–2 on aggregate.
Zürich won 6–3 on aggregate.
Brann won 1–0 on aggregate.
Wisła Kraków won 7–2 on aggregate.
Vejle won 6–0 on aggregate.
1–1 on aggregate; Strømsgodset won 4–2 on penalties.
3–3 on aggregate; Anderlecht won on away goals.
3–3 on aggregate; Rapid Wien won on away goals.
Grazer AK won 3–0 on aggregate.
Dynamo Moscow won 2–0 on aggregate.
Hajduk Split won 3–2 on aggregate.
Sigma Olomouc won 4–0 on aggregate.
Wisła Kraków won 5–0 on aggregate.
1–1 on aggregate; Slavia Prague won 5–4 on penalties.
Bologna won 4–1 on aggregate.
Willem II won 6–0 on aggregate.
2–2 on aggregate; CSKA Sofia won on away goals.
Dynamo Moscow won 5–4 on aggregate.
Fiorentina won 2–1 on aggregate.
Aston Villa won 6–2 on aggregate.
Grazer AK won 3–1 on aggregate.
3–3 on aggregate; Red Star Belgrade won 4–3 on penalties.
Werder Bremen won 4–2 on aggregate.
Zürich won 7–2 on aggregate.
Marseille won 6–2 on aggregate.
Real Sociedad won 5–2 on aggregate.
Stuttgart won 4–3 on aggregate.
Vitesse won 6–3 on aggregate.
Monaco won 3–1 on aggregate.
Grasshoppers won 2–0 on aggregate.
Club Brugge won 7–2 on aggregate.
Bordeaux won 3–2 on aggregate.
Atlético Madrid won 3–0 on aggregate.
Parma won 3–2 on aggregate.
Celtic won 4–2 on aggregate.
Roma won 3–0 on aggregate.
Liverpool won 8–0 on aggregate.
Bayer Leverkusen won 2–1 on aggregate.
Lyon won 3–2 on aggregate.
Celta de Vigo won 8–0 on aggregate.
Real Betis won 5–1 on aggregate.
Valencia won 7–3 on aggregate.
1–1 on aggregate; Leeds United won 4–1 on penalties.
Rangers won 5–3 on aggregate.
Bologna won 4–1 on aggregate.
Bordeaux won 3–1 on aggregate.
Parma won 3–2 on aggregate.
Club Brugge won 4–3 on aggregate.
AS Monaco won 7–3 on aggregate.
Real Sociedad won 6–2 on aggregate.
Zürich won 5–3 on aggregate.
Lyon won 5–3 on aggregate.
The match was abandoned at half-time after the fourth official, Philippe Flament of Belgium, sustained a knee injury and bruising from a firecracker thrown onto the pitch by fans in the stands. At the moment of the incident, Fiorentina led 2–1 on the night and 4-1 on aggregate. Four days later at a UEFA emergency meeting, Fiorentina was kicked out of the UEFA Cup and the match was recorded as a 0–3 Grasshopper win. Future expulsion from European competition for Fiorentina was also considered by UEFA but eventually ruled out because of mitigating circumstances, specifically that the match, as part of an earlier punishment, was not played at Fiorentina's home stadium but in Salerno and credible evidence that the firecracker was likely thrown by fans of the local club Salernitana holding a grudge following a recent Serie A fixture between the two clubs.[2]
Grasshopper won 3–2 on aggregate.
Celta de Vigo won 3–2 on aggregate.
Marseille won 4–3 on aggregate.
Roma won 1–0 on aggregate.
Atlético Madrid won 5–2 on aggregate.
2–2 on aggregate; Liverpool won on away goals.
Real Betis won 4–1 on aggregate.
Rangers won 3–2 on aggregate.
Parma won 4–2 on aggregate.
Bologna won 4–2 on aggregate.
Lyon won 5–3 on aggregate.
3–3 on aggregate; Bordeaux won on away goals.
Roma won 3–2 on aggregate.
Celta de Vigo won 4–1 on aggregate.
Marseille won 3–2 on aggregate.
Atlético Madrid won 5–3 on aggregate.
Parma won 7–2 on aggregate.
Bologna won 3–2 on aggregate.
Atlético Madrid won 4–2 on aggregate.
Marseille won 2–1 on aggregate.
1–1 on aggregate; Marseille won on away goals.
Parma won 5–2 on aggregate.
