In 1962, Rowley's interest in cancer and chromosomes was sparked as an NIH trainee, studying the pattern DNA replication in normal and abnormal human chromosomes. Dr. Rowley then returned to the University of Chicago, as a research associate in the Department of Hematology. She became an associate professor in 1969 and a full professor in 1977. In the 1970s, she further developed the use of existing methods of quinacrine fluorescence and Giemsa staining to identify chromosomes, and demonstrated that the abnormal Philadelphia chromosome implicated in certain types of leukemia was involved in a translocation with chromosome 9 in some cases. Translocation is the process by which a piece of one chromosome breaks off and joins another chromosome, or when two chromosomes exchange material when both break. She also identified translocation between chromosomes 8 and 21 in acute myelogenous leukemia, and between 15 and 17 in promyelocytic leukemia. Rowley also aided in the discovery, through her research, of the formation of retinoid acid, a drug that is able to help return normal function to certain protein receptors.