‌‌Dr. Bavoil's research includes the pathogenesis of multiple species of the obligate intracellular pathogen, Chlamydia. Research areas include comparative genomics within the Chlamydiaceae, the role of the chlamydial type III secretion system in pathogenesis and development, the impact of Chlamydia phage infection on disease, the role of the polymorphic membrane protein family of C. trachomatisin infection and disease, and studies of the triangular relationship between vaginal ecology, pathogenomic properties of the infecting chlamydiae and disease outcome in the infected host.

Drs. Patrik Bavoil and Jacques Ravel are co-Directors of the NIH-NIAID-funded STI Cooperative Research Center "Ecopathogenomics of Chlamydial Reproductive Tract Infection" (EPCRTI).  EPCRTI includes the recruitment and documentation of the CHARM cohort of Chlamydia trachomatis-infected patients, led by Dr. Mishka Terplan (University of Marland, Baltimore - School of Medicine, studies in animal models of human genital disease led by Dr. Roger Rank (University of Arkansas for Medical Sciences), biological informatics and biostatistics resources directed by Dr. Owen White (University of Maryland, Baltimore -Institute for Genome Sciences), omic characterizations of the cervico-vaginal microbiota and of chlamydiae led by Drs. Jacques Ravel and Garry Myers (University of Maryland, Baltimore -Institute for Genome Sciences) and Dr. Larry Forney (University of Idaho), studies of the physiology of infecting chlamydiae led by Dr. Anthony Maurelli (The Henry M. Jackson Foundation), and studies of the host-pathogen interaction led by Dr. Bavoil and biomathematician Dr. David Wilson (University of New South Wales, Australia).

Dr. Bavoil is Chief-Editor of the journal Pathogens and Disease of the Federation of European Microbiological Societies (FEMS) President of the Chlamydia Basic Research Society (CBRS).