Dr. Lynch's focus is on the prevention of healthcare associated infections (HAI), rational use of antimicrobials, and employee health at Harborview Medical Center. In addition, he is an atttending physician in HMC Infectious Diseases Clinic where he sees patients with a broad spectrum of infectious diseases.

Current and recent research projects are focused on the epidemiology of HAI, appropriate infectious disease diagnosis, testing and treatment pathways, risk factors for Clostridium difficile infection, the use of antimicrobials, healthcare worker influenza vaccination, and preventable injury of healthcare workers.