Bautista played in 11 games for the Pirates in 2005. In 2006, his first full season in the major leagues, Bautista hit .235 with 16 home runs (HR) and 51 runs batted in (RBI). The following season in 2007, he posted similar numbers in 142 games, finishing the season with a batting average of .254, 15 home runs and 63 RBI. That same year, he became the starting third baseman for the Pittsburgh Pirates. He took over for reigning National League batting champion Freddy Sanchez, who moved to second base.