Rats are the source of numerous pathogens responsible for significant human morbidity and mortality in cities globally. Despite evidence that rats are thriving in cities, there is little contemporary research on urban rats and rat-associated health risks in Canada. To address this gap, the Vancouver Rat Project captured 725 rats over the course of one year from Vancouver’s Downtown Eastside to study the ecology of rat-associated pathogens. During Phase I of the project, rats underwent a full necropsy and ectoparasites were removed from the fur. Rat tissues were tested for zoonotic organisms using various techniques, including PCR, ribotyping, and whole-genome sequencing. We isolated several pathogens including Bartonella spp., Clostridium difficile, Leptospira interrogans, and methicillin-resistant Staphylococcus aureus. However, certain pathogens thought to be endemic in rats worldwide (e.g., Seoul hantavirus and Rickettsia typhi) were conspicuously absent. Additionally, rats were infested with fleas, lice, and mites; this is important because fleas are known vectors for certain zoonotic bacteria. Prevalence of rat pathogens and ectoparasites varied by block, with some blocks having many infected/infested rats and others having none. This uneven distribution may be a result of local rat population structure, and suggests that the likelihood of contacting a rat and its pathogens is site-specific. To investigate this hypothesis, in Phase II of the project we are performing a genetic analysis of rats to infer population structure and movement patterns of rats, and relating these to environmental features of the capture site. Ongoing research also includes sequencing of flea-associated bacteria to determine whether rat fleas carry known or novel zoonotic pathogens. By integrating data on rat ecology, parasites, and pathogens we aim to better understand rat-associated public health risks – information that can be used in turn to inform programs that monitor and mitigate impacts of rats in the urban environment.