In recent years, quantitative molecular diagnostic assays based on real-time PCR have been developed for many pests and pathogens of potato. In addition, simple sequence repeat markers have been developed and used to track isolates of Phytophthora infestans. These diagnostic assays are now being used as tools to study unresolved questions in the epidemiology of potato diseases including late blight, powdery scab and black dot. Examples of various investigations designed to examine the relative contribution of seed and soil-borne inoculum in causing black dot and powdery scab on progeny tubers, the effect of environmental factors on the incidence and severity of powdery scab and the survival of asexual and sexual inoculum of P. infestans in soil are described. Consideration is given to the development of appropriate diagnostic assays, their use in conjunction with relevant and robust sampling techniques, and the interpretation of results to inform disease risk assessment and control strategies through industry collaboration.