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Vanderputten played college basketball at Pepperdine during the 1992-93 season, then continued with the Waves through the 1995-96 campaign in the West Coast Conference.

Vanderputten arrived at Pepperdine after a U.S. high school season at Trabuco Hills High, where he was an exchange student from Perth, averaged 20.4 points and 11 rebounds as a senior, earned Times Orange County first-team recognition, and helped Trabuco Hills win the Southern Section II-A title before committing to Pepperdine in May 1992 over a group that included Fresno State, Utah, Charlotte, Syracuse, San Diego and Arizona State.

As a freshman in 1992-93, Vanderputten appeared in 22 games and finished with 29 points (1.3 points per game) and 30 rebounds (1.4 per game) while shooting 11-for-28 from the field (39.3%), going 0-for-0 from three, and making 7-of-14 free throws (50.0%), adding 2 assists, 3 steals, and 5 blocks as Pepperdine went 23-8 overall and 11-3 in WCC play under head coach Tom Asbury.

In the 1993-94 season, Vanderputten suited up for Pepperdine on a 19-11 team under head coach Tom Asbury that won the WCC Tournament and reached the NCAA Tournament, where the Waves pushed No. 3 Michigan to overtime before falling 78-74 on March 17, 1994, with Vanderputten playing 30 games and making 15 starts while totaling 120 points (4.0 per game), 97 rebounds (3.2 per game), and 11 blocks (0.4 per game) in 406 minutes (13.5 per game), shooting 45-for-90 from the field (50.0%) with 0-for-0 from three and 30-of-50 at the foul line (60.0%), plus 13 assists, 11 steals, 42 turnovers and 70 fouls.

Vanderputten’s role expanded again in 1994-95 as he appeared in all 27 games and started 26, averaging 21.7 minutes while producing 219 points (8.1 points per game) and 142 rebounds (5.3 per game) on 89-for-163 shooting (54.6%), with no three-point attempts, and 41-of-58 free throws (70.7%), along with 15 assists, 10 steals and 24 blocks (0.9 per game), and he finished that year with 45 turnovers and 55 fouls as Pepperdine closed 8-19 and exited the WCC tournament with a 52-62 loss to Portland in the neutral-site opener on March 4.

As a senior in 1995-96, Vanderputten played in 28 games and averaged 7.4 points and 5.8 rebounds per game while also leading the WCC in blocks at 1.5 per game, including a single-game high of six blocks against Cal State Northridge on December 5, 1995, and that season also included a coaching change in which David A. Wilson served as interim head coach for Pepperdine’s final 13 games.

Across four seasons at Pepperdine, Vanderputten appeared in 107 games and scored 576 points (5.4 per game), finishing as a multi-year frontcourt contributor who moved from a limited freshman role into regular starts by his second and third seasons and capped his college career with conference-leading rim protection as a senior.