The Program in Molecular Biophysics aims to involve students in research projects from the start. First-year students complete three 10-week rotations in laboratories of their choosing. By summer of the first year, students join a lab and embark on thesis research. Beginning in the fifth semester, students meet annually with a faculty thesis review committee.

Although PMB faculty members come from many departments, all students in the program are enrolled in one of only two departments. All first-year students enroll in the Thomas C. Jenkins Department of Biophysics in the School of Arts and Sciences located on the Homewood campus.

If a student chooses a thesis adviser from the School of Medicine or the School of Public Health (on the East Baltimore campus), that student transfers enrollment in the second year to the Department of Biophysics and Biophysical Chemistry, School of Medicine. Academic policy and requirements are the same for all PMB students, regardless of departmental affiliation.

PMB core courses are taught at Homewood and East Baltimore and approximately half of the PMB faculty is affiliated with each campus. A free shuttle runs between the two locations. Many students live within walking distance of the Homewood campus and take the shuttle to East Baltimore as needed.

The Homewood campus, a 140-acre wooded area in central Baltimore, is home to the Krieger School of Arts and Sciences and the Whiting School of Engineering. The East Baltimore campus encompasses the Johns Hopkins Medical Institutions (JHMI) including the School of Medicine, the Bloomberg School of Public Health, and the Johns Hopkins Hospital.