Background: Adults with polycystic ovary syndrome (PCOS) can have multiple metabolic abnormalities. However, studies in the adolescent population are still limited and these results seem to vary widely. This study was to investigate the metabolic abnormalities in adolescents with PCOS in South China and the potential risk factors contributed to these health risks. Methods: Anthropometric measurements and biochemical parameters were evaluated in 128 adolescents with PCOS and their age-and BMI-matched controls. Results: The prevalence of pre-diabetes, insulin resistance, hyperinsulinemia, dyslipidemia and metabolic syndrome in adolescents with PCOS was 11.7%, 46.9%, 29.7%, 22.7% and 4.7%, respectively. 16.3%, 74.4%, 67.4%, 39.5% and 14% of the PCOS subjects with BMI > 85th had pre-diabetes, insulin resistance, hyperinsulinemia, dyslipidemia and metabolic syndrome, whereas 9.4%, 32.9%, 10.6%, 14.1% and 0% of the PCOS subjects with BMI < 85th had such disturbances. Conclusions: Adolescents with PCOS in South China had more metabolic abnormalities than their age-and BMI-matched non-PCOS counterparts. Obesity could worsen insulin resistance, hyperinsulinemia and metabolic syndrome in PCOS adolescents.