Viruses are the leading cause of foodborne illness associated with the consumption of raw or slightly cooked contaminated shellfish. The aim of this study was to evaluate the prevalence of hepatitis A virus in molluscs. Standard and real-time reverse transcription-polymerase chain reaction procedures were used to monitor bivalve molluscs from the Granada fish markets (southern Spain) for this human enteric virus. Between February 2009 and October 2010, we collected a total of 329 samples of different types of bivalve molluscs (mussels, smooth clams, striped venus, and grooved clams). The results showed the presence of hepatitis A virus in 8.5% of the 329 samples analyzed. We can therefore confirm that conventional fecal indicators are unreliable for demonstrating the presence or absence of viruses. The presence of hepatitis A virus in molluscs destined for human consumption is a potential health risk in southern Spain.