48 teams (national domestic cup champions, plus the best qualified teams from the most important European national domestic leagues), entered a preliminary group stage, divided into eight groups of six teams each, and played a round-robin. The final standings were based on individual wins and defeats. In the case of a tie between two or more teams, after the group stage, the following criteria were used to decide the final classification: 1) number of wins in one-to-one games between the teams; 2) basket average between the teams; 3) general basket average within the group.
The top four teams from each group qualified for a 1/16 Final Playoff (X-pairings, home and away games), where the winners advanced further to 1/8 Finals, 1/4 Finals, and 1/2 Final.
The Final was played at a predetermined venue.
Country ranking
For the 1999–2000 FIBA Saporta Cup, the countries are allocated places according to their place on the FIBA country rankings, which takes into account their performance in European competitions from 1996–97 to 1998–99.[1]
* Tatami Rhöndorf (3rd in the previous season of Bundesliga) merged with Skyliners Frankfurt (at that time newly formed club), so Skyliners took their place in the competition.