The Chicago White Sox selected Thomas with the seventh pick in the first round of the June 1989 Major League Baseball draft. He made his major league debut on August 2, 1990, against the Milwaukee Brewers at County Stadium; he went without a hit, going 0 for 4, but had an RBI on a fielder's choice which scored Iván Calderón as the White Sox won the game 4–3. On August 28 Thomas hit the first home run of his career in a road game against the Minnesota Twins at the Metrodome (which, coincidentally, would also be the site of his 500th career home run). He hit the home run off pitcher Gary Wayne in the top of the ninth inning as his team lost 12–6.