In October 2005, individual donation nucleic acid amplification testing (ID-NAT) for HIV, HBV and HCV was introduced in the Western Cape Province of South Africa. After 5 years, the impact on HIV, HBV and HCV transmission risk was assessed. A total of 649745 donations were tested by ID-NAT using the Ultrio assay on the Tigris instrument (Novartis Diagnostics) and for anti-HIV, HBsAg and anti-HCV (Abbott Prism). Initial reactive samples were repeated in duplicate. Discrepant repeat reactive samples were subjected to confirmatory assays. ID-NAT nonrepeat reactive donations were further screened for occult HBV infection (OBI) by anti-HBc assay. ID-NAT yielded 6 HIV-RNA-positive donations in the anti-HIV-negative window period (WP) but only 2 were p24 Ag nonreactive (1:325000). Mathematical modelling estimated a similar HIV transmission risk for lapsed and repeat donations, in the order of 3 per million. The WP risk for HBV was 13 per million. Eight acute (1:81000) and 13 chronic OBI yield cases (1:50000) were interdicted. There were significantly more anti-HBc-positive donors in the Ultrio initial reactive/nonrepeat reactive group (12%) than in an Ultrio nonreactive control group (6%). ID-NAT in the Western Cape Province of South Africa has contributed significantly to enhancing blood safety, particularly for HBV transmission risk and to a lesser extent for HIV. Anti-HBc testing of NAT nonrepeat reactive donations seems useful in identifying a subgroup of donors with OBI who may be at risk of transmitting HBV.