| 1º Fase | ||||||
| 6/9/88 | Reykjavik | Valur | 1 | Eovaldsson | ||
| Monaco | 0 | |||||
| 5/10/88 | Montecarlo | Monaco | 2 | Vogel, Weah | ||
| Valur | 0 | |||||
| 6/9/88 | Berlin | Dinamo Berlin | 3 | Doll, Thom, Pastor | ||
| Werder Bremen | 0 | |||||
| 11/10/88 | Bremen | Werder Bremen | 5 | Kutzop (P), Hermann, Riedler, Burgsmuller, Schaaf | ||
| Dinamo Berlin | 0 | |||||
| 7/9/88 | Hamrun | Hamrun Spartans | 2 | Leo Refalo (2) | ||
| Nentori | 1 | Shegli | ||||
| 5/10/88 | Tirana | Nentori | 2 | Hodja, Josa | ||
| Hamrun Spartans | 0 | |||||
| 7/9/88 | Larisa | AEL | 2 | Agoroiannis, Mitsibonas | ||
| Xamax | 1 | Hermann | ||||
| 5/10/88 | Neuchatel | Xamax | 2 | Lei Ravello (P), Luthi | ||
| AEL | 1 | Karapialis | ||||
| 7/9/88 | Larnax | Pezoporikos | 1 | Livathinos | ||
| Goteborg | 2 | Eriksson, Ravelli | ||||
| 5/10/88 | Gotemburgo | Goteborg | 5 | Nilsson, Zetterlund, Holmgren, Froberg (2) | ||
| Pezoporikos | 1 | Livathinos | ||||
| 7/9/88 | Praga | Sparta Praga | 1 | Kukleta | ||
| Steaua | 5 | Lacatus (2), Hagi (2), Stoica | ||||
| 5/10/88 | Bucarest | Steaua | 2 | Hagi, Lacatus | ||
| Sparta Praga | 2 | Bilek (2) | ||||
| 7/9/88 | Budapest | Honved | 1 | Fodor | ||
| Celtic | 0 | |||||
| 5/10/88 | Glasgow | Celtic | 4 | Stark, Walker, McAvennie, McGhee | ||
| Honved | 0 | |||||
| 7/9/88 | Moscu | Spartak | 2 | Ivanov, Shalimov | ||
| Glentoran | 0 | |||||
| 5/10/88 | Belfast | Glentoran | 1 | Moore | ||
| Spartak | 1 | Cherenkov | ||||
| 7/9/88 | Dundalk | Dundalk | 0 | |||
| Estrella Roja | 5 | Mrkela, Musemic, Stojkovic, Stosic, Durovski | ||||
| 5/10/88 | Belgrado | Estrella Roja | 3 | Sabanadzovic, Mrkela, Savicevic | ||
| Dundalk | 0 | |||||
| 7/9/88 | Viena | Rapid | 2 | Kranjcar, Kienast | ||
| Galatasaray | 1 | Savas | ||||
| 5/10/88 | Estambul | Galatasaray | 2 | Tanju, Cuneyt | ||
| Rapid | 0 | |||||
| 7/9/88 | Brujas | Brujas | 1 | Bettagno | ||
| Brondby | 0 | |||||
| 5/10/88 | Copenhague | Brondby | 2 | Frank, Christensen | ||
| Brujas | 1 | Brylle | ||||
| 7/9/88 | Madrid | Real Madrid | 3 | Losada, Tendillo, Butragueño | ||
| Moss | 0 | |||||
| 5/10/88 | Moss | Moss | 0 | |||
| Real Madrid | 1 | Butragueño | ||||
| 7/9/88 | Sofia | Vitosha | 0 | |||
| Milan | 2 | Virdis, Gullit | ||||
| 6/10/88 | Milan | Milan | 5 | Van Basten (4), Virdis | ||
| Vitosha | 2 | Nachev, Zliev | ||||
| 8/9/88 | Zabrze | Gornik | 3 | Warzycha, Urban (2) | ||
| Jeunesse | 0 | |||||
| 5/10/88 | Esch-sur-Alzette | Jeunesse | 1 | Theis | ||
| Gornik | 4 | Komornicki, Urban (2), Zagorski | ||||
| 8/9/88 | Oporto | Oporto | 3 | Madjer, Sousa, Rui Aguas | ||
| HJK | 0 | |||||
| 5/10/88 | Helsinki | HJK | 2 | Valla, Kanerva | ||
| Oporto | 0 | |||||
| 2º Fase | ||||||
| 26/10/88 | Glasgow | Celtic | 0 | |||
| Werder Bremen | 1 | Wolter | ||||
| 9/11/88 | Bremen | Werder Bremen | 0 | |||
| Celtic | 0 | |||||
| 26/10/88 | Bucarest | Steaua | 3 | Dumitrescu, Hagi (2, 1P) | ||
| Spartak | 0 | |||||
| 9/11/88 | Moscu | Spartak | 1 | Cherenkov | ||
| Steaua | 2 | Lacatus, Balint | ||||
| 26/10/88 | Tirana | Nentori | 0 | |||
| Goteborg | 3 | Froberg, Ingesson, Nilsson | ||||
| 9/11/88 | Gotemburgo | Goteborg | 1 | Froberg | ||
| Nentori | 0 | |||||
| 26/10/88 | Eindhoven | PSV Eindhoven | 5 | Kieft, Ellerman, R. Koeman (2), Janssen | ||
| Oporto | 0 | |||||
| 9/11/88 | Oporto | Oporto | 2 | Rui Aguas, Domingos | ||
| PSV Eindhoven | 0 | |||||
| 26/10/88 | Brujas | Brujas | 1 | M'Buyu | ||
| Monaco | 0 | |||||
| 9/11/88 | Montecarlo | Monaco | 6 | Fofana (3), Sonor, Toure (2) | ||
| Brujas | 1 | Audoor | ||||
| 26/10/88 | Neuchatel | Xamax | 3 | Luthi, Chassot, Decastel | ||
| Galatasaray | 0 | |||||
| 9/11/88 | Estambul | Galatasaray | 5 | Ugur (2), Tanju (3) | ||
| Xamax | 0 | |||||
| 26/10/88 | Milan | Milan | 1 | Virdis | ||
| Estrella Roja | 1 | Stojkovic | ||||
| 9/11/88 | Belgrado | Estrella Roja | 1 | Bajic | ||
| (*) | Milan | 0 | ||||
| 10/11/88 | Belgrado | Estrella Roja | 1(2) | Stojkovic | ||
| Milan | 1(4) | Van Basten | ||||
| (*) Partido suspendido a los 65' por niebla, jugado desde el comienzo al dia siguiente | ||||||
| 26/10/88 | Chorzow | Gornik | 0 | |||
| Real Madrid | 1 | Sanchez (P) | ||||
| 10/11/88 | Madrid | Real Madrid | 3 | Sanchez (2), Butragueño | ||
| Gornik | 2 | Jegor, Baran | ||||
| 4º Final | ||||||
| 1/3/89 | Goteborg | Gotemburgo | 1 | Ingesson | ||
| Steaua | 0 | |||||
| 15/3/89 | Bucarest | Steaua | 5 | Lacatus (3), Dumitrescu, Balint | ||
| Gotemburgo | 1 | Zetterlund | ||||
| 1/3/89 | Eindhoven | PSV Eindhoven | 1 | Romario | ||
| Real Madrid | 1 | Butragueño | ||||
| 15/3/89 | Madrid | Real Madrid | 2 | Sanchez (P), Vazquez | ||
| PSV Eindhoven | 1 | Romario | ||||
| 1/3/89 | Bremen | Werder Bremen | 0 | |||
| Milan | 0 | |||||
| 15/3/89 | Milan | Milan | 1 | Van Basten (P) | ||
| Werder Bremen | 0 | |||||
| 1/3/89 | Montecarlo | Monaco | 0 | |||
| Galatasaray | 1 | Tanju | ||||
| 15/3/89 | Colonia | Galatasaray | 1 | Prekazi | ||
| Monaco | 1 | Weah | ||||
| SEMIFINALES | ||||||
| 5/4/89 | Bucarest | Steaua | 4 | Dumitrescu, Hagi (P), Petrescu, Balint | ||
| Galatasaray | 0 | |||||
| 19/4/89 | Esmirna | Galatasaray | 1 | Cuneyt | ||
| Steaua | 1 | Dumitrescu | ||||
| 5/4/89 | Madrid | Real Madrid | 1 | Sanchez (P) | ||
| Milan | 1 | Van Basten | ||||
| 19/4/89 | Milan | Milan | 5 | Ancelotti, Rijkaard, Gullit, Van Basten, Donadoni | ||
| Real Madrid | 0 | |||||
| FINAL | ||||||
| 24/5/89 | Barcelona | Milan | 4 | Gullit (2), Van Basten (2) | ||
| Steaua | 0 | |||||
| Campeón: MILAN (ITALIA) | ||||||