Molecular epidemiology is a relatively new branch of epidemiology that uses molecular biology methods to study health and disease in populations. This article gives an introduction to molecular epidemiologic terminology and methodology and its usefulness in large animal medicine and veterinary public health. Applications in source tracing and vaccine studies and insights into transmission dynamics, host specificity, and niche adaptation of infectious organisms are presented. Examples are drawn from a variety of diseases, organisms, and host species and range from the global level to the individual-animal level.