Abstract Aim of the study was the evaluation of the effect of heat treatment in shellfish experimentally contaminated with human Norovirus (NoV). Feline Calicivirus (FCV), often used as surrogate for human NoV, was examined in parallel to test for virus infectivity after treatment. The experiments were performed subjecting suspensions and spiked mussels to heat treatment (60 °C and 80 °C) for various times. Analysis by rRT-PCR showed a limited reduction of NoV (less than 1 log RT-PCR units ml−1) and FCV (0.3–1.2 log TCID50 ml−1) both in virus suspensions and in spiked mussels, with the exception of NoV suspensions treated at 80 °C (reduction of 3 log RT-PCR units ml−1). Cell culture assay showed that the infectious FCV in suspensions decreased of 4 log after 3 min of treatment while a lower reduction (2 log) was obtained in spiked samples treated for 15 min. Data showed that mussel matrix plays a protective role against heat inactivation of viruses. Despite the efficacy of rRT-PCR for viral nucleic acid detection, its inability to provide information on virus infectivity, represents a limit to the evaluation of product safety. Caution should therefore be used in the evaluation of efficacy of heat treatments on virus-contaminated foods and when the judgment of food product safety is based exclusively on rRT-PCR results.