Polycystic ovary syndrome (PCOS) is a heterogeneous endocrine disorder with individual susceptibility determined by genetic and environmental risk factors. Recently, studies have evaluated the CAPN10 gene in PCOS patients, suggesting that different alleles may play a role in PCOS susceptibility. We performed a cross-sectional study with 88 southern Brazilian hirsute patients with PCOS or idiopathic hirsutism (IH) to assess the influence of CAPN10 genetic variants on clinical and biochemical features of metabolic syndrome. PCOS patients were defined by oligo/amenorrheic cycles (<9 cycles/year), increased levels of serum testosterone and/or free androgen index, and exclusion of other disorders associated with hyperandrogenism. IH was diagnosed in hirsute patients with regular ovulatory cycles (luteal-phase progesterone levels >3.8 ng/ml), normal androgen levels, and without any known underlying disease (n = 29). Metabolic syndrome was defined according to the 2001 criteria of the National Cholesterol Education Program, Adult Treatment Panel III. UCSNP-43 polymorphism of CAPN10 was related to metabolic syndrome (p = 0.047) in PCOS; UCSNP-19 and UCSNP-63 were not associated with phenotypic traits in PCOS. These results provide evidence that CAPN10 gene UCSNP-43 polymorphisms may influence the PCOS metabolic phenotype. This should be further confirmed in large population-based studies.