After the 2003 season, the Baltimore Orioles selected Bautista in the Rule 5 draft and carried him on their Opening Day roster. He made his MLB debut with Baltimore on April 4, 2004. After playing 16 games with the Orioles, the Tampa Bay Devil Rays claimed him off waivers on June 3. Twenty-five days later, the Kansas City Royals purchased him from Tampa Bay after a 12-game stint with the Devil Rays. He played 13 games for the Royals before they traded him to the New York Mets on July 30 for Justin Huber, who then traded him minutes later to Pittsburgh with Ty Wigginton and minor leaguer Matt Peterson for Kris Benson and Jeff Keppinger. This series of transactions made him the first player to appear on five different Major League Baseball rosters in one season, only since matched by Oliver Drake in 2018. (Drake, however, actually played for all five teams, while Bautista only played for four; he never actually suited up or played for the Mets.)