AbstractHuman leukocyte antigen‐E (HLA‐E) is an important nonclassical major histocompatibility complex (MHC) class I (Ib) molecule that acts as the ligand for NKG2A/B/C receptors expressed on natural killer (NK) cells and T cells. Unlike the classical class I molecules, HLA‐E is highly conserved in evolution and the biological significance of polymorphism is therefore unclear. Our aim was to investigate the polymorphism in HLA‐E gene in three ethnic groups in the UK and to obtain population data relating to any variations observed at this locus. We developed a polymerase chain reaction–sequence‐specific primer (PCR‐SSP) method for identifying HLA‐E single nucleotide polymorphisms (SNPs) in genomic DNA. This was used to investigate the genotype distribution and allele frequency of nine published SNPs in the coding region of HLA‐E in 223 Euro‐Caucasoid, 60 Afro‐Caribbean and 52 Asian healthy individuals. Genotype frequencies were in Hardy–Weinberg equilibrium. No polymorphism was observed for seven previously reported SNPs and these should not be considered polymorphic. However, positions 1114 and 1446 were confirmed as polymorphic and different genotype frequencies were identified at nucleotide position 1114 between the three studied ethnic groups. We present these data together with the intragene haplotype frequencies in these populations. To our knowledge, this is the first description of population frequencies of nine different SNPs in HLA‐E in three main large ethnic groups. The data generated from this study will be of importance in the context of describing the effect of HLA‐E polymorphism in clinical settings such as transplantation and autoimmune diseases.