The Microbiology Department offers programs leading to the Master of Science and Doctor of Philosophy degrees, and also participates actively in the Five College Ph.D. Program. For graduate study in microbiology extensive undergraduate courses in microbiology are not as essential as a strong undergraduate background in chemistry, biological sciences, mathematics, and physics. Normally it is expected that entering graduate students will have completed two semesters each of organic chemistry, biochemistry, and physics, and mathematics through calculus. Students with deficiencies in these courses must compensate for them by taking appropriate courses as early as possible. Students may register for graduate courses while correcting deficiencies.

The general requirements for the M.S. and Ph.D. degrees in microbiology are those of the Graduate School. In addition, general GRE scores are required. The department requires no foreign language reading competency for the doctorate. Upon entrance a student meets with the Graduate Program Director to plan the first-year course schedule. By the end of the second semester the student should select a research area. Subsequently, the research adviser helps plan the remainder of the course program.

A comprehensive examination is administered between the third and fourth semesters of graduate study. It consists of both written and oral parts and is designed to evaluate the extent to which students have acquired a working knowledge of the principles of microbiology.

By the end of their third year, students orally defend a proposal of the entire dissertation project in the dissertation prospectus in front of the chosen Dissertation Committee.

Ph.D. candidates in Microbiology must have at least one first-authored manuscript published or 'in press' in a professional peer-reviewed journal from their dissertation research before scheduling their dissertation defense.