Abstract:  HLA class‐I and class‐II allele frequencies and two‐locus haplotypes were examined in 367 unrelated Melanesians living on the islands of Vanuatu and New Caledonia. Diversity at all HLA class‐I and class‐II loci was relatively limited. In class‐I loci, three HLA‐A allelic groups (HLA‐A*24, HLA‐A*34 and HLA‐A*11), seven HLA‐B alleles or allelic groups (HLA‐B*1506, HLA‐B*5602, HLA‐B*13, HLA‐B*5601, HLA‐B*4001, HLA‐B*4002 and HLA‐B*2704) and four HLA‐C alleles or allelic groups (HLA‐Cw*04, HLA‐Cw*01, HLA‐Cw*0702 and HLA‐Cw*15) constituted more than 90% of the alleles observed. In the class‐II loci, four HLA‐DRB1 alleles (HLA‐DRB1*15, HLA‐DRB1*11, HLA‐DRB1*04 and HLA‐DRB1*16), three HLA‐DRB3‐5 alleles (HLA‐DRB3*02, HLA‐DRB4*01 and HLA‐DRB5*01/02) and five HLA‐DQB1 alleles (HLA‐DQB1*0301, HLA‐DQB1*04, HLA‐DQB1*05, HLA‐DQB1*0601 and HLA‐DQB1*0602) constituted over 93, 97 and 98% of the alleles observed, respectively. Homozygosity showed significant departures from expected levels for neutrality based on allele frequency (i.e. excess diversity) at the HLA‐B, HLA‐Cw, HLA‐DQB1 and HLA‐DRB3/5 loci on some islands. The locus with the strongest departure from neutrality was HLA‐DQB1, homozygosity being significantly lower than expected on all islands except New Caledonia. No consistent pattern was demonstrated for any HLA locus in relation to malaria endemicity.