Established in 1979, the Department of Microbiology is headed by Dr. Neeta Khandelwal and offers 25 NMC-recognised postgraduate seats annually. Located on the second floor of the college, it houses seven well-equipped specialty laboratories — Bacteriology, Serology, the Viral Research and Diagnostic Laboratory (VRDL), the HIV State Reference Laboratory, OPD diagnostics, CD4, TORCH and Mycology, and the Polio and Measles laboratory.

All diagnostic services are NABL accredited (since 2011, currently covering 47 tests) and the Polio laboratory is a WHO-accredited national referral laboratory. The department functions as the State Nodal and Referral Centre for Antimicrobial Resistance Surveillance, HIV testing, the Integrated Disease Surveillance Programme and the AIIMS–NCDC–ICMR Healthcare-Associated Infection Surveillance Network — one of the largest in the country. It is an integral member of the Hospital Infection Control and Antimicrobial Stewardship committees, with quality-management SOPs maintained to international standards.

The department participates in nearly 20 national and international health programmes under WHO, NCDC and ICMR. Long-running initiatives include the WHO-accredited National Polio Surveillance Project (since 1995) and projects across NACP, the National Vector Borne Disease Control Programme, Measles and Rubella surveillance, Influenza-like Illness surveillance, the National AMR Containment Programme, the National Viral Hepatitis Control Programme, scrub typhus and leptospirosis surveillance, dengue and chikungunya genomic surveillance, and the WHO Typhoid Surveillance Project.

During the COVID-19 pandemic, the VRDL operated 24×7 and has processed close to one million RT-PCR tests to date. Following the tragic flight crash of 12 June 2025, the department worked alongside the Civil Hospital team to collect samples for DNA matching at FSL/NFSU, enabling timely identification and return of remains to bereaved families.