In 1984, Dr. Rowley was made the Blum-Riese Distinguished Service Professor of medicine, cell biology, molecular and human genetics at the University of Chicago. She also served as the interim deputy dean for science. In 1989, she was not only presented with the Charles S. Mott Prize by General Motors Cancer Research Foundation, but the Clowes Memorial Award as well. In 1991, she was elected as a member into the American Philosophical Society. In 1998, she was one of three scientists awarded the prestigious Lasker Award for their work on translocation, and received the National Medal of Science in 1998.