Lazio won the final against Mallorca to earn their only title in the competition.

Chelsea were the defending champions, but were eliminated in the semi-finals by Mallorca.

TH Title Holders Rudar Velenje won 2–0 on aggregate.

3–3 on aggregate; Apollon Limassol won on penalties.

The game was played in Brussels as Genk's stadium did not meet UEFA requirements.

Before the game, the Heart of Midlothian delegate complained about the non-standard goal height, and the referee measured it to be 1 centimetre lower than regulation.

Heart of Midlothian agreed to play the game anyway.

The game was played in Brussels as Genk's home stadium did not meet UEFA requirements.

Genk raised an official protest, claiming that the corner locations are too close to the fence around the pitch.

[citation needed] 1–1 on aggregate; Mallorca won on away goals.

The top scorers from the 1998–99 UEFA Winners' Cup (including qualifying round) are as follows: