Purpose Polycystic ovary syndrome (PCOS) is one of the most encountered endocrine malfunctions. PCOS patients have enhanced activation of the blood coagulation system. Methods Eighty-six young women with PCOS and 70 healthy control women were included in our study. PCOS patients and controls were matched for age, body mass index, and allele frequency. Genetic analysis of TPAI and PAI-1 were performed in all subjects. Results and conclusions No statistically significant differences have been detected about the ratios of genotypes resulting from PAI-1 promotor 4G/5G gene polymorphism. PAI-1 765 4G/5G gene polymorphism and TPA gene's Alurepeat insertion/deletion (I/D) polymorphism ratios were not different from the controls. In this study it is shown by the analysis of TPA gene's Alu-repeat insertion/deletion (I/D) polymorphism the PCOS patients with genotype II had lowers total cholesterol and LDL-cholesterol levels.