The 1999 NCAA Division I baseball tournament was played at the end of the 1999 NCAA Division I baseball season to determine the national champion of college baseball. The tournament was expanded to 64 teams for 1999, adding a Super Regional. The tournament concluded with eight teams competing in the College World Series, a double-elimination tournament in its fifty third year. Sixteen regional competitions were held to determine the participants in the final event, with each winner advancing to a best of three series against another regional champion for the right to play in the College World Series. Each region was composed of four teams, resulting in 64 teams participating in the tournament at the conclusion of their regular season, and in some cases, after a conference tournament. The fifty-third tournament's champion was Miami (FL), coached by Jim Morris. The Most Outstanding Player was Marshall McDougall of Florida State University.

National seeds

Bold indicates CWS participant.

Regionals and super regionals

Bold indicates winner.

Coral Gables Super Regional

Tallahassee Super Regional

Columbus Super Regional

Waco Super Regional

Tuscaloosa Super Regional

Stanford Super Regional

College Station Super Regional

Houston Super Regional

Hosted by Rice at the Astrodome

College World Series

Participants

Results

Bracket

Game results

All-Tournament Team

The following players were members of the College World Series All-Tournament Team.

Notable players