 Whiteside was considered a "long shot" to make the Orioles'roster in 2006, but he remained in spring training with the Orioles until they made their final cuts on April 1 and sent him to Ottawa. On May 21, Whiteside had four RBI in a game against the Rochester Red Wings, and he had back-to-back three-hit games against the Norfolk Tides from July 23 through 24. In 92 games (315 at bats) with Ottawa in 2006, Whiteside batted .244 with 77 hits, 11 home runs, and 47 RBI. His batting average was .281 at home compared to .201 on the road. In 2007, Whiteside attended spring training but was reassigned to the minors on March 27, coinciding with the Orioles' acquisition of Alberto Castillo. Whiteside began the season with the Orioles' Triple-A affiliate, which was now the Norfolk Tides, but after he batted .180 in 18 games he was reassigned to Bowie on May 11. He spent time on the disabled list from June 18 through July 12 with a fractured right cheekbone. Upon returning, he had a seven-game hitting streak, but he was lost for the season on August 6 after suffering a concussion. In 42 games (141 at bats) with Bowie, Whiteside hit .291 with 41 hits, four home runs, and 30 RBI. After 2007, he filed for free agency, having played in only nine major league games during his seven years with the Orioles.
