Polycystic ovary syndrome (PCOS) affects around 15% of Indigenous women who are also a group at high risk of cardiometabolic disease.To explore the impact of PCOS on metabolic syndrome in Indigenous women.A cross-sectional reproductive health questionnaire, biochemical and anthropometric assessments, of 109 Indigenous women (35 with PCOS and 74 without PCOS) aged 15-44 years in and around Darwin between 2003 and 2005. PCOS was defined using the National Institutes of Health criteria, and metabolic syndrome (MetS) using the National Cholesterol Education Programme Adult Treatment Programme III criteria. The outcome was prevalence of MetS by PCOS status; relationship of PCOS with MetS before and after adjustment for markers of obesity and insulin resistance.Women with PCOS had a significantly higher body mass index (BMI) (P = 0.0001) and MetS was more frequent in women with PCOS (51%) than those without PCOS (23%) (P = 0.003). The most frequent components of MetS in both groups were a high density lipoprotein cholesterol ≤1.29 mmol/L (80% PCOS, 55% non-PCOS) and a waist circumference >88 cm (77% PCOS, 41% non-PCOS); these were significantly more frequent in women with PCOS (P = 0.01). In logistic regression models, PCOS was significantly associated with MetS by itself but not after adjustment for BMI or sex hormone binding globulin.While MetS was more common in Indigenous women with PCOS, PCOS was not an independent predictor of MetS. This may be because obesity and insulin resistance are integral parts of PCOS and are the mechanisms through which PCOS exerts metabolic effects.