Norovirus (NoV) is recognised as one of the most common causes of foodborne infections, and shellfish are a well-documented source of this virus. The presence of NoV in shellfish has not previously been investigated in Turkey, and hence the aim of this study was to determine the frequency of human NoV genogroups I and II in mussels collected from the Bosphorus, Istanbul, Turkey. A total of 320 mussels representing 110 samples originating along the Bosphorus coast were collected from fish distributors. RNA was extracted using the RNeasy Mini Kit and real-time RT-PCR performed using primers specific for NoV genogroup I and II. Amongst the 110 samples, 5 (4.5%) were found to be positive for NoV genogroup II by SYBR Green assay; no genogroup I was detected. A positive signal was obtained by SYBR Green for NoV Genogroup II in mussels collected in October, November and December 2008, and February and July 2009. Only four out of five SYBR Green positive samples could be confirmed by the use of a NoV GII probe-based real-time RT-PCR. The average count and SD of Enterobactericaeae, E. coli and sulphide reductase anaerobic bacteria in PCR positive mussels were 3.56 log +/- 0.96 log, 2.32 log +/- 0.77 log and 1.70 log +/- 0.56 log, respectively. This study shows that NoV Genogroup II is present in mussels collected from the Bosphorus, Istanbul, and may constitute a risk to human health.