Polycystic ovarian syndrome (PCOS) is associated with insulin-induced plasminogen activator inhibitor-1 (PAI-1) elevations. Since thrombophilic states correlate with high miscariage rates, as does PCOS, this study aimed at looking for thrombophilic predisposition in PCOS women compared with non-PCOS controls.The prevalence of antithrombin III, protein S and protein C deficiencies, as well as factor V Leiden, prothrombin G20210A factor and methylene tetrahydrofolate reductase (MTHFR) mutations, was compared between two different groups of women, one with PCOS (n = 30) and one without PCOS (n = 45).Median proportions of activated protein C, S and antithrombin III as well as the activated protein C ratios were within normal ranges in both samples. There was no evidence that the genetic analysis for factor V Leiden or prothrombin factor differed between the two samples. The odds ratio (OR) of bearing a mutation on the MTHFR gene was 1.2-fold higher [95% confidence interval (CI) 0.470-3.065] in women with PCOS than in women without (P = 0.83). Although this difference is not statistically significant, it might indicate a slightly higher prevalence of heterozygous genotypes in women with PCOS (OR = 1.197, 95% CI 0.473-3.034).Molecular risk factors of hereditary thrombophilia do not show increased prevalence in women with PCOS in comparison with women in the general population. The existence of a possible trend towards higher prevalence of MTHFR mutation in women with PCOS needs further study, particularly regarding homocysteine levels.