The environmental route of transmission is important for many protozoan and helminth parasites, with water, soil and food being particularly significant. Both the potential for producing large numbers of transmissive stages and their environmental robustness (with the ability to survive in moist microclimates for prolonged periods of time) pose persistent threats to public and veterinary health. Increased demands made on natural resources increase the likelihood of encountering environments and produce contaminated with parasites. In the last 30 years, endemic and epidemic waterborne and foodborne outbreaks in developed countries have led to a reappraisal of conventional isolation and detection methods. While these methods have proved invaluable in our understanding of environmental transmission routes for helminths, they have been less effective for the parasitic protozoa. Robust, efficient detection, viability and typing methods are required to assess risk and to further epidemiological understanding. Greater awareness of parasite contamination of our environment and its impact on health has precipitated the development of better detection methods. Currently, nowhere is this more apparent than with Cryptosporidium, with a broad range of immunological, microscopical and molecular methods available. The upsurge in molecular techniques, particularly the polymerase chain reaction, for determining occurrence and viability have brought with them the added benefits of increased sensitivity and specificity, yet many methods still have to be shown to address these issues consistently in the field. Rapid commercialization of reagents and standardization of methods provide consistency. The advances identified in non-destructive and destructive methods for the protozoa have application for helminths and emerging pathogens and should determine the importance of the matrices involved in the environmental transmission of parasites, further safeguarding public and veterinary health.