Objective. To study the genomic variations of a hepatitis B virus (HBV) isolate in a patient coinfected with human immunodeficiency virus type 1 (HIV-1) who developed severe hepatitis and died of AIDS. Methods. Two blood samples were collected, the first one during the asymptomatic phase of HIV-1 infection, and the other, 3 years later, few months before the death of the patient. Both samples were HBsAg and anti-HBe positive. Pre-S/S and precore-core genome regions were PCR amplified and analyzed. Results. The HBV isolate belonged to genotype F, cluster IV. A number of unique amino acid substitutions were found in the surface antigen gene and the overlapping polymerase coding region of HBV genomes derived from both samples. However, these substitutions reflected natural variations rather than mutations of clinical significance. The precore stop codon mutation A1896 was present in both genomes. Furthermore, the HBV genome derived from the second, but not first sample, showed two out-of-frame core interval deletions, one and 103 nucleotides in length, respectively. Conclusions. This is the first report of an HBV isolate from genotype F with core internal deletions. Our results suggest an association between specific core mutations and the severe hepatitis developed by the patient.