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The Challenge Cup tournament was discontinued and the new format featured 23 teams – 9 from Lithuania, 8 from Estonia, 5 from Latvia and 1 from Kazakhstan. For the Regular season the teams were divided into three groups of six and one group of five. Top four teams of each group advanced to Last 16 where they were divided into four groups. Two best teams of each group advanced to the play-offs. All play-off games were played in home-and-away series.
Ventspils became the first ever Latvian team to win the tournament by beating Lithuanian side Prienai 161–142 on aggregate score in the finals. Kalev/Cramo from Estonia won their first Baltic League medal by downing Latvian side Barons kvartāls 144–137 in the bronze medal playoffs.
Teams
Key to colors
Champion
Runner-up
Third place
Fourth place
Quarterfinalist
Last 16
Regular season
Country (League)
Teams
Teams (rankings in 2011–12 national championships)
^ Head-to-head record and head-to-head point differential were equal, therefore overall point differential in Last 16 phase was used to determine the group winner
In the knockout phase rounds will be played in a home-and-away format, with the overall cumulative score determining the winner of a round. Thus, the score of one single game can be tied.