Polycystic ovary syndrome (PCOS) is a heterogeneous condition with unknown etiology and is considered to be the most common endocrine disorder in women of reproductive age. Two meta-analyses are presented here concerning the association of Plasminogen Activator Inhibitor 1 (PAI-1) 4G/5G polymorphism and the methylene-tetrahydrofolate reductase (MTHFR) C677T polymorphism with the risk of developing PCOS. Seven studies were included concerning PAI-1 (1538 cases, 710 controls) and six studies concerning MTHFR C677T (223 cases, 392 controls). Overall, a significant association was found for PAI-1, with the odds ratio (OR) for 4G carriers versus 5G homozygotes being equal to 1.600 (95% CI 1.052, 2.434) with strong evidence for dominant inheritance. There was however a large between-studies variability (I(2) = 67.3%). No evidence was found for association of MTHFR C677T polymorphism with PCOS (OR for the TT+CT versus CC comparison equal to 0.940 with 95% CI 0.561, 1.575). No evidence of publication bias was found in these meta-analyses. PAI-1 4G/5G polymorphism seems to be associated with the risk of developing PCOS. Further studies are needed in order to investigate the etiologic mechanism behind this association, as well as the interrelations with other components of the metabolic syndrome (hypertension, diabetes, etc.).