Background Serological typing of HLA has shown discrepancies in HLA associations with vitiligo in different ethnic populations.Objectives To perform genotyping of HLA class II genes on a Dutch vitiligo population in order clearly to identify susceptible and protective HLA alleles in vitiligo.Methods HLA typing was carried out by amplifying genomic DNA by polymerase chain reaction (PCR) followed by dot-blot hybridization with sequence-specific oligonucleotides (SSO). Fifty Dutch vitiligo probands, and their parents (150 individuals) and 204 healthy controls were studied.Results Family-based case–control association studies and linkage disequilibrium analysis showed the linkage and association of DRB4*0101 allele with vitiligo (Pc = 0·0016, relative risk = 2·21). The family-based association study also provided evidence for linkage and association of DQB1*0303 allele with vitiligo (χ2 = 7·36, P = 0·006). We measured the clinical relevance of the test by calculating the prevalence corrected positive predictive values (PcPPV). The PcPPV of disease for the DRB4*0101 allele was 0·017 and for the DRB4*0101/0101 genotype was 0·0358. In other words, a DRB4*0101/0101 genotype carries a 3·58% risk of developing vitiligo.Conclusions Both DRB4*0101 and DQB1*0303 alleles provide significant susceptibility for vitiligo.