Whiteside came to Marshall University under the radar during the start of the 2009–10 season, but it did not take long for him to make national attention. He was spotlighted in the December 28 edition of ESPN The Magazine's College Basketball column after he amassed 14 points, 17 rebounds and nine blocked shots over 29 minutes in a 60–53 win over the Ohio University Bobcats on November 28. A few weeks later on December 12, Whiteside recorded the Thundering Herd's first triple-double in a 105–54 rout of the Brescia Bearcats, scoring 17 points, grabbing 14 rebounds and blocking 11 shots. Whiteside would go on to have two more triple-doubles on the year against the UCF Knights on January 13, and February 27. He finished the season as the nation's leader in blocked shots with 182, and he also broke the C-USA record held by Tulsa's Jerome Jordan for most blocked shots in a single season and the Marshall record for the most blocked shots in a single season and career all in his freshman year. The 182 blocks were also a national record for a freshman in a single season, topping 177 by BYU's Shawn Bradley in 1990–91.