After the 1996 season, the Tigers traded Nitkowski with Brad Ausmus, José Lima, Trever Miller, and Daryle Ward to the Houston Astros for Doug Brocail, Brian Hunter, Todd Jones, Orlando Miller, and cash. After the 1998 season, the Astros traded Nitkowski with Ausmus back to the Tigers for Paul Bako, Dean Crow, Brian Powell, and minor-leaguers Carlos Villalobos and Mark Persails. Late in the 2001 season, the Tigers traded Nitkowski to the New York Mets for a player to be named later, later identified as minor-leaguer Kyle Kessel.