During his time in Buffalo, Winkelstein studied the health impact of the city's air pollution, successfully separating the effect of pollution from other confounding social and environmental factors, and also contributed greatly to the understanding of coronary artery disease in women.
[5] At Berkeley, Winkelstein did pioneering research on the link between tobacco smoke and cervical cancer.
Winkelstein led the San Francisco Men's Health Study, one of the largest and best-described cohorts of people at risk for HIV/AIDS.
[5][6] Winkelstein also addressed Peter Duesberg's arguments that AIDS was related to drug use rather than HIV infection, demonstrating, along with immunologist Michael Ascher and other colleagues, that "such claims have no basis in fact.
"[7][8] Since retiring and assuming emeritus status, Winkelstein worked on biographical sketches of major figures in the history of epidemiology, including John Snow, Edward Jenner, and his mentor, Abraham Lilienfeld.