Houtteman was the youngest major leaguer in 1946 but played only one game for the Tigers that season, allowing eight runs and fifteen hits in eight innings. He spent most of 1946 in the minor leagues, finished at 16–13 and led the league in strikeouts. At the end of the season, Houtteman was named by six of the eight International League managers as the top pitching prospect in the league, leading the league in strikeouts with 150, pitching over 200 innings, finishing second in victories with 16, and amassing an 11–2 road record. Minor league third baseman Johnny Bero liked Houtteman's fielding ability so much that he called him "a fifth infielder."