The 1999 Conference USA baseball tournament was the 1999 postseason baseball championship of the NCAA Division I Conference USA, held at USA Stadium in Millington, Tennessee, from May 12 through 17.
Tulane defeated Houston in the championship game, earning the conference's automatic bid to the 1999 NCAA Division I baseball tournament.
[2] Two play-in games among the four teams with the worst regular season records decided which two teams would have the final two spots in the eight-team double-elimination bracket.