Though the activities of this department can be said to have commenced with the starting of the Plague Research Laboratory in 1896, a separate Department of Clinical Pathology was established in the year 1905. From its very inception the department undertook studies on plague, diagnostic and investigational studies on almost the entire range of communicable  diseases like cholera, malta fever (Brucellosis), typhoid, malaria, diphtheria, relapsing fever etc. which in their epidemic forms brought devastation to the mankind. The department covered a wide range of laboratory functions and was concerned with the diagnosis, patient care, and prevention of diseases.

Under the leadership of Director of Haffkine Institute, this department has been revamped as per GLP norms providing facilities of clean room, tissue culture laboratory etc.    

At present Department is actively involved in Training, Research and Testing activities. Department participates in training programmes like Annual Biotechnology Training. Department also train students for M.Sc. and Ph.D. degree in Microbiology and Applied Biology affiliated to Mumbai University and MUHS, Nasik.

Department is actively involved in  research on various infectious diseases like Tuberculosis, Methicillin Resistant Staphylococcus Aureus (MRSA), Extended Spectrum β- Lactamase (ESBL) and Metallo β- Lactamase (MBLs). Department is also involved in biosynthesis of nano particles, checking anti-bacterial activity of  Kombucha (Chinese tea) and Caffeine, development of diagnostic tests for Tuberculosis and herbal anti tuberculosis compounds, research in autoimmune disorder (Scleroderma) in collaboration with National Institute of Immunohematology The department also carries out anti-bacterial and antifungal activities of different fruit juices.

The department has well established testing laboratory where following test are conducted like, hematology, serology, bacteriology and mycology. It receives clinical samples from E.S.I.S. hospitals, govt. hospitals and public health dispensaries. Department also conducts antimicrobial, antimycobacterial and antifungal testing of synthetic compounds developed by the research centers, colleges and pharmaceuticals Department conducts bacteriological investigation of post fumigation Operation theatre swabs received from Civil Hospitals, Sub-District Hospitals, various Primary Health Care Centers and rural hospitals.

The department has future plan of conducting training program on Scientific Writing Pharmaceutical Microbiology and Animal Tissue Culture.Department has also planned training for health care workers on Operation Theatre Infection Control and Prevention,. The department has future plan to reintroduce various histopathological and cytological examination of biopsy specimens and serological tests for diagnosis of auto-immune diseases and other infectious diseases.