Retiring from the Menninger Foundation in 2001, Menninger became the chairman of Menninger Trustees. The Menninger Clinic moved from Topeka to Houston in 2003, becoming affiliated with Baylor College of Medicine. While his older brother Roy was bothered by the move, Walt Menninger backed the change in location. Consultants had recommended that the clinic be moved to an urban area near a medical school and an airport. In 2000, Walt Menninger had said that the clinic would be out of business in a few years unless it moved. In the summer of 2001, negotiations between Menninger and Baylor College of Medicine were briefly called off, but the two institutions were able to work out an affiliation before the move.