Since October 2005, all blood units collected in South Africa were screened individually for human immunodeficiency virus (HIV)-1, hepatitis B and C virus (HBV, HCV) genomes uncovering preseroconversion window period (WP) infections for each virus and occult HBV infections (OBIs) defined as persistent HBV DNA without detectable hepatitis B surface antigen (HBsAg). Samples identified as HBsAg-negative/DNA-positive were confirmed by combining real-time quantitative polymerase chain reaction, nested amplification, anti-HBc and anti-HBs. Amplified basic core promoter/precore, pre-S/S, and whole genome were sequenced, analyzed, and compared to 73 HBsAg+ strains. Genotype was determined by phylogenetic analysis. From 109 samples examined, 54 were classified as OBI, 14 as WP, 20 as false-positive, five as other classification, and 16 as undetermined due to lack of serological or follow-up data. OBI donors were predominantly males (67%), median age 31 years, black (54%), with normal alanine aminotransferase levels. Viral load ranged between unquantifiable and 518 IU/mL (median 5 IU/mL). Genotype A1 was more frequent (23 strains) than genotype D (seven strains). Genotype A1 strains were little mutated. In the major hydrophilic region, 56.5% strains were wild type or with few amino acid substitutions. Most important, all 13 full genome sequences presented 1 to 7 mutations known to or assumed to negatively impact viral replication. In particular, 6/13 sequences had a stop codon in the HBx gene translated into deletion of 117 or 19-25 C-terminus amino acids not found in 15 HBeAg+ HBsAg+ strains. One WP sequence with an HBx stop codon suggested infectivity. Conclusion: Genotype A1 OBIs are different from genotype A2 and D OBIs in that there is little evidence of immune pressure as a major factor involved in OBI genesis. Limited replication appears mostly related to genetic viral defects. (HEPATOLOGY 2009.)