With only 21 years of age, Villegas debuted in MLS with the then called NY/NJ Metrostars. Later he played with the New Jersey Stallions of the USISL. In 1999, he was drafted again by the Metrostars in the MLS Supplemental Draft. He played with the team until 2002 when he was traded to DC United. In 2003, he returns to his homeland aiming to earn a spot on the National Team roster. He played that season with Club Aucas. In 2004, he played with Barcelona de Ecuador, team in which he played the Copa Libertadores. Later on, he played with Deportivo Cuenca, who were the National Champions in 2004. He joined the Islanders in May 2005, having an immediate impact on the team.  He played in 23 games, scoring 6 goals and 6 assists for a total of 18 points. He was recognized in Team of the Week #10, 16 and 21, being Player of the Week #10. He was also recognized by the USL in the All-League Second Team. In 2006, Villegas moved up to the forward position where he appeared in 19 games scoring 2 goals and 3 assists. He returns in 2007 for his third consecutive season with the Islanders.