Villegas began playing on the PGA Tour in 2004 and earned his PGA Tour card just prior to the 2006 season. He had a blistering start to his 2006 rookie year on tour, with two second-place finishes and a third place (at The Players Championship) in his first nine events. He missed making the 2006 Masters Tournament in his rookie year by a single position on the Official PGA Tour Money List (11th). However, he made his first Masters' appearance in 2007 by finishing in the top 40 of the Official PGA Tour Money List for 2006. He qualified for the 2008 Masters through his exceptional play during the inaugural FedEx Cup playoff system, that included an opening round 63 (8 under par) at the Deutsche Bank Championship and three straight top 10 finishes. He entered the FedEx Cup playoffs in 52nd place and improved to 28th place through his play in the first three events, thus qualifying for the 30-man field at The Tour Championship in Atlanta, Georgia, where he finished in the top 10 for the third straight week and finished 24th on the FedEx Cup points list.