Noroviruses, hepatitis A and E viruses, sapovirus, astrovirus, rotavirus, Aichi virus, enteric adenoviruses, poliovirus, and other enteroviruses enter shellfish through contaminated seawater or by contamination during handling and processing, resulting in outbreaks ranging from isolated to epidemic. Processing and disinfection methods include shellfish depuration and relaying, cooking and heat pasteurization, freezing, irradiation, and high pressure processing. All the methods can improve shellfish safety; however, from a commercial standpoint, none of the methods can guarantee total virus inactivation without impacting the organoleptic qualities of the shellfish. Noroviruses cause the majority of foodborne viral illnesses, yet there is conflicting information on their susceptibility to inactivation by processing. The inability to propagate and quantitatively enumerate some viral pathogens in vitro or in animal models has led to the use of norovirus surrogates, such as feline calicivirus and murine norovirus. During processing, these surrogates may not mimic the inactivation of the viruses they represent and are, therefore, of limited value. Likewise, reverse transcription-PCR has limited usefulness in monitoring processing effectiveness due to its inability to identify infectious from inactivated viruses. This article (a) describes mechanisms of virus uptake and persistence in shellfish, (b) reviews the state-of-the-art in food processing strategies for the inactivation of enteric viruses in shellfish, (c) suggests the use of combined processing procedures to enhance shellfish safety, (d) highlights limitations in research data derived from virus surrogate studies and molecular assay procedures, and (e) recommends enhanced funding for human volunteer studies and the development of assays to detect viable viruses.