 Thornton played college baseball for Grand Valley State University and was drafted by the Seattle Mariners in the first round as the 22nd overall pick in 1998 MLB draft.Thornton played briefly (only pitched 1 inning) with the Single A Everett AquaSox in the Northwest League.In and , Thornton was a starting pitcher with the Wisconsin Timber Rattlers in the Midwest League and showed improvement with his ball control and accuracy, striking out nearly 1 batter an inning.