The department of Medical Microbiology is situated at the School of Medicine at the College of Health Sciences. It serves the Schools of Medicine, Nursing, Pharmacy, and Dental Sciences. Besides teaching undergraduate students of these faculties, the department teaches medical microbiology to postgraduate students from departments of Pathology, Surgery and University of Nairobi Institute of Tropical and Infectious Diseases.
Medical Microbiology offers 2 postgraduate courses: Post graduate diploma in Sexually Transmitted Infections and Masters of Science in Medical Microbiology.