1999 NCAA Division I baseball tournament

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.
 * 1) Miami (FL)
 * 2) Florida State
 * 3) Cal State Fullerton
 * 4) Baylor
 * 5) Alabama
 * 6) Stanford
 * 7) Texas A&M
 * 8) Rice

Regionals and super regionals
Bold indicates winner.

Houston Super Regional
Hosted by Rice at the Astrodome

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

Notable players

 * Alabama: Andy Phillips
 * Cal State Fullerton: Adam Johnson, Kirk Saarloos
 * Florida State: Kevin Cash, Matt Diaz
 * Miami (FL): Bobby Hill, Mike Neu
 * Oklahoma State:
 * Rice:
 * Stanford: Joe Borchard, Tony Cogan, Justin Wayne
 * Texas A&M: Casey Fossum