The Yale-New Haven Medical Center provides a rich clinical, educational, and research environment for fellowship training in medical microbiology.

The fellowship is centered at the Clinical Microbiology laboratory of Yale-New Haven Hospital. The laboratory provides state-of-the-art diagnostic microbiology services to the hospital's inpatient and outpatient care programs, which include active bone marrow, stem cell, and solid organ transplantation programs, HIV/AIDS care, cancer center, trauma center, and an active Tropical Medicine clinic.

Yale-New Haven Hospital is a primary clinical campus for Yale University School of Medicine. The medical school faculty has active research projects in many areas related to infectious disease. A partial list would include projects studying the pathogenesis of intracellular protozoal infections, molecular pathways of macrophage action, gene regulation of HIV infection and production of novel anti-HIV therapies, RNA metabolism in African trypanosomes, host-pathogen interactions in Salmonella infection, processing and presentation to T lymphocytes of antigens derived from intracellular pathogens, pathogenesis of pathogenesis of invasive fungal disease, and intracellular survival of Legionella, as well as many others. A wide variety of clinical research projects in infectious disease, especially protocols related to AIDS care, are ongoing at the medical center.