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This is a partial list of conference champions from the 1961 season. Each of the eight geographical districts chose, by various methods, the team that would represent them in the NCAA tournament. 9 teams earned automatic bids by winning their conference championship while 16 teams earned at-large selections.
The 1961 season marked the fifteenth NCAA baseball tournament, which culminated with the eight team College World Series. The College World Series was held in Omaha, Nebraska. The eight teams played a double-elimination format, with Southern California claiming their third championship with a 1–0 win over Oklahoma State in the final.