Human and animal fecal wastes and urine contain a large number of different viruses that can enter the environment through the discharge of waste materials from infected individuals. Despite the high diversity of viruses that are introduced into the environment by human fecal pollution, only a few have been recognized to cause disease in association with consumption of contaminated shellfish. Viruses are present in shellfish in very low numbers. Nevertheless, they are present in sufficient quantities to pose a health risk as presented. This low level of contamination has made it necessary to develop highly sensitive viral extraction methods to ensure virus recovery from shellfish tissues. The most common route for accidental contamination is after heavy rainfall, leading to overflow and release of untreated sewage into the aquatic environment. To limit shellfish contamination the most desirable and effective option is to reduce the viral input.