Vagelos deferred military service while in medical school, but he was obligated to serve a two-year stint as an Army doctor. As a Columbia University College of Physicians and Surgeons trained physician, Vagelos obtained a two-year assignment as a scientist at the National Institutes of Health (1956–1966). For Vagelos, it was a fateful turning point. He was associated with Massachusetts General Hospital, Washington University and the Washington University School of Medicine (1966–1975) before joining Merck, Sharp & Dohme Research Laboratories in Rahway.