HLA-A2-positive nasopharyngeal carcinoma (NPC; n = 38) and normal control (n = 51) populations were analysed by high-resolution oligotyping to identify A2 allelic microvariants. Within the control group, A*0207 was found to be the most common allele, accounting for 50% of the A2 frequency in normals. In contrast, this allele was found to be present in only 23% of NPC cases, suggesting a protective effect. Of these 9 NPC patients with A*0207, all were associated with B46, unlike in the control group, where it can be found associated with non-B46 antigens. Another allele, A*0201, which was thought to be protective against NPC was in fact present in 39.5% of NPC patients, more than twice the frequency in controls. These data confirm that A*0201 is not a protective allele for NPC, and other factors such as the A*0207, non-B46 haplotype are of greater importance.