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Objective: Polycystic ovary syndrome (PCOS) in adolescents is associated with adverse metabolic outcomes. The association of menstrual irregularity with metabolic risk among adolescents with PCOS was assessed. Method: A retrospective medical record review of 366 adolescents with PCOS aged 13-18 years was conducted, from which 265 girls newly diagnosed with PCOS were included and divided into those presenting with primary amenorrhea (PA), secondary amenorrhea (SA) and oligomenorrhea (OM). Androgen concentrations and markers of metabolic risk were compared among the groups. Results: Most subjects presented with OM (PA = 17, SA = 30 and OM = 218). Subjects with PA were younger than those with OM but not different from those with SA. Mean BMI was not different between groups. Total testosterone and insulin levels were higher in PA than SA and OM (p < 0.01 and 0.02, respectively). Fasting glucose was higher in PA than OM (p = 0.048) but not different from SA. Triglyceride levels were higher in PA than SA and OM (p < 0.001 each). More subjects with PA and SA had metabolic syndrome (52%) than those with OM (29.1%) (p = 0.027). The differences in triglycerides and glucose persisted despite BMI adjustment in multivariate regression models. Conclusion: Adolescents with PCOS presenting with PA are at risk of metabolic disease beyond expected based on BMI.