Viral outbreaks attributed to the consumption of contaminated shellfish have been clearly demonstrated. Thirty-five samples of mussels collected from areas with two different levels of faecal pollution were analysed for somatic coliphages, F-RNA phages and bacteriophages infecting Bacteroides fragilis HSP40 and RYC2056 following standardised protocols, and for enterovirus, human adenovirus and hepatitis A virus by nucleic acid amplification (Nested-PCR and RT-PCR). Four methods for viral recovery from shellfish have been compared. The first method is based on borate buffer at pH 9.5 as eluent, the second is based on glycine buffer at pH 10 as eluent, a third method is based on glycine buffer at pH 7.5 and changes in conductivity and the fourth method on nutritive broth with Tween 80 as eluent. The results obtained were analysed statistically and the method based in glycine buffer at pH 10 seems to be the most efficient and useful for the recovery of phages and human viruses. The results also show a different pattern in the proportions between the viral parameters when the source of the faecal pollution is close to or distant from the shellfish growing area.