Endometriosis is a common gynaecological disorder due to ectopic implantation of endometrial tissue. It is manifested by pelvic inflammation and abrogation of cell-mediated immunity and may be also characterised by autoantibody production, thus suggesting that endometriosis might be an autoimmune disorder. Genetic factors also play a role in the aetiopathogenesis of this disease. Therefore, the present study was aimed at testing the association of endometriosis with the PTPN22/LYP 1858C> T gene polymorphism, which appears to be related to the development of a variety of autoimmune disorders. The study included 171 Polish patients of Caucasian origin with laparoscopically and histopathologically confirmed endometriosis and 310 unrelated, ethnically matched control individuals. DNA and serum were isolated from the peripheral blood. The PTPN22/LYP 1858C> T polymorphism was typed using a PCR-RFLP method. Anti-nuclear (ANA) and anti-cardiolipin (ACA) autoantibodies were detected by the Hep-2 indirect immunofluorescence test and a specific ELISA respectively. No statistically significant differences were found in distribution of C and T PTPN22/LYP alleles and genotypes in patients with endometriosis compared with the control population. However, on exploratory analyses we noted that the PTPN22/LYB T allele and the TT genotype may be associated with the prevalence of double positivity for ANA and ACA (p=0.003 by chi(2) test for trend and p=0.009 by Fisher's exact test respectively). The results of the present study show that endometriosis in a Polish population is not associated with the PTPN22/LYP 1858C> T gene polymorphism. The putative effect of the PTPN22/LYP genotype on the development of autoantibodies is potentially interesting, but it should be verified in further studies.