Objective: To compare clinical and metabolic features of adolescents having primary amenorrhea (PA) and polycystic ovarian syndrome (PCOS) with those having oligomenorrhea or secondary amenorrhea (OM/SA) and PCOS. Design: Retrospective case-control study. Setting: Endocrine Gynecology Clinic at The Hospital for Sick Children, Toronto, Ontario, Canada. Patients: Girls and young women aged 14 to 18 years having PA and PCOS (n=9) seen during a 2 1/2-year period were compared with control subjects having OM/SA and PCOS (n=18) randomly selected during the same period. Intervention: Medical record review was performed to assess clinical, biochemical, and ultrasonographic measures, as well as response to a progesterone challenge. Main Outcome Measures: Differences in response to the progesterone challenge, hyperandrogenism, and the presence of features of the metabolic syndrome. Results: Compared with adolescents having OM/SA, adolescents having PA demonstrated older age at pubarche, higher androstenedione levels, greater prevalence of family history of obesity, a tendency toward no withdrawal bleeding in response to the progesterone challenge, and more features associated with the metabolic syndrome (acanthosis nigricans, higher diastolic blood pressure, and lower high-density lipoprotein cholesterol level). No significant correlation was demonstrated between response to the progesterone challenge, metabolic features, and androstenedione levels. Conclusion: Adolescents with PA and PCOS exhibit increased features of the metabolic syndrome and higher androstenedione levels and may represent a more severe spectrum of a common condition.