The Department of Microbiology was established in 1962 as the Department of Bacteriology under the Headship of Prof Chapman, Head of Department at the Faculty of Medicine, Colombo. Very soon after, in 1963, the department became independent with Prof (then Dr) S.N. Arsecularatne transferred from the Faculty of Medicine, Colombo to join the permanent staff of the Faculty of Medicine, University of Ceylon, Peradeniya.

The department is involved in undergraduate teaching to medical, vet and allied health science undergraduates through conducting lectures, small group discussions, seminars, practicals, and bench training.

The Department of Microbiology contributes to the postgraduate teaching through the MSc in Medical Microbiology offered by PGIS, University of Peradeniya and MD in Medical Microbiology offered by PGIM, University of Colombo. In addition, the department offers research training to students to obtain M.Phil and Ph.D. degrees depending on the availability of expertise and resources.