Despite his perennial offensive production and established fan base in Chicago, the White Sox elected to release Thomas in 2005. Thomas later expressed disappointment with how his 16-year tenure with the White Sox was ended, saying that chairman Jerry Reinsdorf did not call him to tell him he wasn't coming back. He also said that he and Kenny Williams did not see eye-to-eye after Williams became general manager following the 2000 season. At the time, Thomas was unhappy that his next-to-last deal with the White Sox contained a "diminished skills" clause. He said the White Sox should have traded him after the playoffs that season.