A total of 47 Caucasian duodenal ulcer patients and 680 healthy persons were investigated for HLA antigens of classes I and II. HLA antigens of the A, B series were sought using the microlymphocytotoxicity test, and HLA-DRBI was analysed by polymerase chain reaction. The study found associations of duodenal ulcer with HLA-A10, -B41 and different combinations of these alleles, whereas HLA-A9 was found to be protective. A relative risk of peptic ulcer was 3.03 in HLA-A10 (pcor < 0.05), and 7.78 in HLA-B41 (p < 0.001). The allele frequency A9 was higher in healthy controls (30.15%) than in Helicobacter pylori-positive patients with duodenal ulcer (10.64%, RR = 3.50, pcor < 0.05). The study showed that frequencies of alleles HLA-DR7 and HLA-A1/B12 were higher in Helicobacter pylori-positive duodenal ulcer patients with family history of peptic ulcer (RR = 4.00 and RR = 11.92, respectively p < 0.05). These data suggest that HLA may influence duodenal ulcer susceptibility and resistance, and according to the high prevalence of Helicobacter pylori (HP) infection in Siberian population (87.5%), this may occur through a non-HP infection pathway.