Molina was originally signed as an undrafted free agent by the Chicago White Sox on January 3, 2000.

He was on the White Sox' opening day roster due to backup catcher Toby Hall being placed on the disabled list.

[1] In December 2007, Molina signed a minor league contract with the New York Mets and became a free agent at the end of the season.

On January 29, 2010 the Boston Red Sox signed Molina to a minor league contract.

Molina signed a minor league contract with an invitation to spring training with the New York Yankees for the 2011 season.