Stephen Baylin attended Duke University, and earned his M.D. degree at its Medical School, where he completed his internship and first year residency in Internal Medicine. Then he worked for two years at the National Heart and Lung Institute of the National Institutes of Health (NIH). In 1971 he joined the departments of Oncology and Medicine at the Johns Hopkins University School of Medicine, an affiliation that still continues.

Presently, he is Deputy Director of the Cancer Center, Professor of Medicine and Professor of Oncology. He is also Chief of the Cancer Biology Division of the Johns Hopkins Oncology Center, and Associate Director for Research of The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins. He has been a member of committees of the American Cancer Society and of NIH, and his honors include a Research Career Development Award from NIH, the Edwin Astwood Lectureship of the Endocrine Society, and appointment to the Virginia and D.K. Ludwig Professorship in Cancer Research and most recently the 2009 Kirk A. Landon-AACR Prize for Basic Cancer Research, also shared with Peter A. Jones, PhD. He is the recently gave 2010 Brecher Lecture at UCSF.

So far, during his highly productive career, Stephen Baylin has authored or co-authored over 300 full-length publications.