In Italy, about 7 % of the resident population is represented by immigrants originating from geographic regions at high endemicity for hepatitis B virus infection. This study aims to assess the prevalence of occult HBV infection (OBI) including the identification of HBV-genotypes in a population of immigrants serologically negative for hepatitis B surface antigen (HBsAg). Between May 2006 and May 2010, 339 immigrants were tested for markers of HBV, hepatitis C virus (HCV) and human immunodeficiency virus (HIV) infections. HBV-DNA was tested by using nested-PCR assays on three different genetic region. HBV-DNA was detected in plasma samples of 11/339 (3.2 %) patients. Most of them had no serological markers of HBV infection, 3/58 (5.2 %) were anti-HBc-alone, and 4/13 (30.8 %) were anti-HIV positive. HIV positivity was the only factor independently associated with the higher probability of observing OBI (OR = 16.5, p < 0.001). No HCV co-infected patients were found. Genotype D was detected in 9/11 (81.8 %) OBI cases, while the remaining two (18.2 %) were classified as genotype E. Although OBI was found at lower rate than expected among immigrants from highly endemic countries, anti-HBc alone positivity was confirmed as a sentinel marker of occult HBV infection. Nevertheless, a marked heterogeneity of HBV markers was found among HBV-DNA positive subjects. Our finding evidenced the predominance of HBV-genotype D viral strains among OBI cases, also in those from geographical areas where overt HBV infections are mainly sustained by viral genotypes other than D.