Although the aetiology of endometriosis remains unclear, many immunological abnormalities involving changes in cell-mediated and humoral immunity may be associated with endometriosis. Several disorders are thought to be associated with particular HLA antigen types. This study examines the possible association between HLA-DQ and DP.A total of 83 patients diagnosed with endometriosis following laparoscopic examination were typed for the HLA-DQB1 and DPB1 alleles using PCR-restriction fragment length polymorphism (RFLP). The HLA DQB1 and DPB1 allele frequencies in these patients and in 222 controls were compared.The prevalence of HLA-DQB1*0301 in the patient group was 16.3% (27/166 alleles), compared with 8.3% in the overall control group (37/444 alleles) and 7.7% in the females of the control group (18/234 alleles). Thus, the prevalence of the HLA-DQB1*0301 allele was significantly greater in patients with endometriosis, compared with the general controls [OR 2.13, 95% CI 1.25-3.64, P = 0.004 (chi(2) analysis), Corrected P-values; Pc = 0.049] and with the general female controls [OR 2.33, 95% CI 1.24-4.39, P = 0.008 (chi(2) analysis), Pc; NS]. There was no significant association in the frequencies of DPB1 alleles between the patients and controls.The HLA systems may be involved in the aetiology of endometriosis, although further study is needed.