The viruses primarily associated with shellfish-borne illness are norovirus, causing gastroenteritis and hepatitis A virus (HAV). Recent years have seen a proliferation of publications on methods for detection of these viruses in shellfish using polymerase chain reaction (PCR). However, currently no standard harmonised procedures have been published. Standardisation is necessary before virus methods can be considered for adoption within a regulatory framework. A European standardisation working group is developing a two-part (quantitative and qualitative) standard method for virus detection in foodstuffs, including shellfish, which has the potential to be incorporated into EU legislation as a reference method. This article describes the development of the standard method and outlines the key methodology principles adopted, the controls and other quality assurance measures supporting the method and future necessary developments in the area.