We describe a novel allele encoding HLA-A23: A*2306, discovered in an African-American individual, whose DNA was HLA typed as part of a quality control exercise. Direct sequencing typing identified A*2301 and A*6601 with an unexpected heterozygous peak at position 331. As position 331 is at the end of exon 2, near the priming site for the B3.6 anti-sense sequencing primer, the sequencing data is not optimal in this region and sequencing from the sense primer is relied on. In addition the new polymorphism was not at an expected polymorphic position and could easily have been missed, leading to the assignment of A*2301. However, data from reference strand mediated conformation analysis showed distinct new mobilities from those expected for A*2301 with two different fluorescent-labelled references, leading to the conclusion that the heterozygous peak seen at position 331 was a true variant of the A*2301 allele. A*2306 is most similar to A*2301 with 1 nucleotide difference at position 331 in exon 2 which was previously a conserved position. This mutation results in an amino acid substitution of glutamine for glutamate at residue 87.