Molina began his professional career with the Johnson City Cardinals of the Rookie-level Appalachian League in 2001, playing 44 total games and batting .259. He advanced one level in each of four seasons in the minor leagues. Even without highly developed offensive skills, Molina proved difficult to strike out. Mainly a singles hitter who favored hitting the ball the other way, he batted .278 with 14 home runs and 133 runs batted in (RBIs) with 118 strikeouts in 1,044 at-bats in four minor league seasons. In his first three seasons, he threw out 111 base runners attempting to steal while allowing 133 stolen bases, for a caught-stealing percentage of 45%.