Meir Stampfer's research revolves primarily around four major prospective studies: the Nurses' Health Study, for which he serves as PI, Nurses' Health Study II, the Health Professionals Follow-Up Study (HPFS), and the Physicians' Health Study (PHS). He served as a founding co-investigator for the latter three cohorts; his work in prostate cancer is based in HPFS and PHS. Biologic samples have been collected in each of the cohorts, sometimes repeatedly. Using a nested case-control design, the samples are analyzed for a variety of markers of disease risk. They use food frequency questionnaires, diet records, anthropometry, and biochemical analyses of serum, plasma, DNA, RNA, red cells, adipose tissue, tumor tissue, and toenails. These studies investigate many health outcomes including cancer and cardiovascular disease.

Most of his teaching is at the Harvard School of Public Health, where he teaches the Practice of Epidemiology. He also served as chair of the Department of Epidemiology 2000-2007, and is PI of two long-standing training grants related to cancer epidemiology.