Mechanisms associated with reactivation of hepatitis B virus (HBV) in patients with occult HBV infection (OBI) remain unclear. In some cases immunosuppression is an enhancer of viral replication. However, not all patients with OBI who undergo immunosuppression experience reactivation. This study explores the role of viral heterogeneity as a determinant of occult HBV reactivation. HBV genotype, mutation patterns and quasispecies were assessed by sequencing the PreS/S region of 16 patients with OBI undergoing chemotherapy, 3 of whom experienced a OBI reactivation. The latter were also assessed at the time of reactivation. Phylogenetic analysis identified low nucleotide and amino acid diversity rates. There were no differences in the viral quasispecies, or common mutation patterns, detected between patients who underwent reactivation of OBI, and those who did not. Furthermore, upon reactivation, the quasispecies evolved towards a loss of most of the variants present during the initial OBI stage, probably representing the fittest version of the virus. The genetic variability of HBV alone did not account for the transition from occult to overt infection, which appears to be governed principally by the host immune response.