Human enteric viruses are able to persist in the environment and can be concentrated by shellfish, leading to outbreaks of gastroenteritis and hepatitis. Developments in molecular biology have allowed the establishment of sensitive and specific methods to detect these viruses. However, preliminary steps to concentrate viral particles and to purify nucleic acids are still needed. Studies using these new tests have demonstrated viral contamination in shellfish from different parts of the world, and some comparisons between the occurrence and seasonality of virus contamination and disease outbreaks can be made. Molecular epidemiology studies have allowed documentation of the origin and spread of disease from contaminated shellfish in some outbreaks by showing sequence identity between amplicons from viruses from environmental and clinical samples. Future application of these methods will continue to be important to further monitor global food safety and understand the natural history and evolution of these important human pathogens.