Freshman season at UConn delayed until Dec. 6, 2003 game against Army while the NCAA determined Villanueva's freshman eligibility; scored 16 points in 22 minutes in that game. Averaged 8.9 points, 5.3 rebounds and was second on the team with 1.5 blocks (behind Emeka Okafor). Named to Big East All-Rookie team.

Committed to Connecticut over Kansas in June 2003. Considered NBA draft before enrolling at UConn. Had committed to Illinois in the fall of 2003 but reopened recruiting when Illini's head coach Bill Self took job at Kansas. Also looked at North Carolina and UCLA.

The Brooklyn, N.Y. native prepped at Blair Academy in Blair, N.J. where he was a consensus All-American as a senior averaging 19 points, 10 rebounds, 4 blocks, 3 assists and 3 steals. He played in the McDonald’s All-American game and the EA Sports Roundball Classic and was named a USA Today All-USA Second Team and New Jersey's Co-Player of the Year. Among ten finalists for the Naismith Prep Player of the Year Award.