Hunter made his major league debut for the Astros on June 27, 1994 against the Cincinnati Reds. In five at bats he contributed with one hit, and stole his first base in this game. He played with Houston through the 1996 season. On December 10 of that year he was traded along with Orlando Miller, Todd Jones and Doug Brocail, as well as cash, to the Detroit Tigers for Daryle Ward, C. J. Nitkowski, Trever Miller, José Lima and Brad Ausmus.