He graduated from Stanford University in 1990 with degrees in Biology, Symbolic Systems, and Classics, and received an M.D. in 1995 from the University of Washington. He completed residency in Internal Medicine at Brigham and Women's Hospital, Harvard Medical School, and was a fellow in Oncology and Hematology at Dana Farber Cancer Institute and the Massachusetts General Hospital. He was awarded a Howard Hughes Medical Institute Physician-postdoctoral fellowship at Dana Farber. Dr. Stamatoyannopoulos then served as Chief Scientific Officer of biotechnology company Regulome Corp., and subsequently joined the Departments of Genome Sciences and Medicine (Oncology) at the University of Washington in 2005. He was elected to American Society for Clinical Investigation in 2009 and is a member of the Editorial Board of Genome Research.