The 34C>G (Prol2Ala) polymorphic variant of the peroxisome proliferator-activated receptor-&#947;2 (PPAR-&#947;2) gene has been associated with polycystic ovary syndrome (PCOS). However, the results between populations are contradictory. Thus, in the present study was investigated the possible association between 34C>G polymorphism at the PPAR-&#947;2 gene and PCOS in Chilean women. A total of 50 unrelated women (29.1 + 8.1 years) with diagnosis of PCOS and 75 healthy controls (29.3+ 9.3 years) were included in this study. Serum lipids, glucose and uric acid levels were determined by enzymatic-colorimetric methods. The 34C>G variant in the PPAR-&#947;2 gene was analyzed by PCR-RFLP. Women with PCOS exhibited a higher levels of glucose, total cholesterol, triglycerides, LDL-C and uric acid, and lower HDL-C levels than controls (p <0.05). The frequency of the 34G alíele was 9% in PCOS patients and 12% in control women (p = 0.589). The odds ratio for PCOS associated with 34G alíele was 0.73 (95% CI = 0.31 - 1.69) confirming the absence of association. We conclude that the 34C>G polymorphism of the PPAR-&#947;2 gene is not related to PCOS in Chilean women