BACKGROUND: Major depressive disorder (MDD) is a common mental disorder, the onset of which frequently occurs during adolescence. While differences in heart rate variability (HRV) between depressed and healthy participants have previously been observed, results have been inconsistent. This study thus investigated the features of HRV in adolescents with MDD. METHODS: We recruited first-episode drug-naive adolescents aged 13-18 years who had been diagnosed with MDD, and healthy age-matched controls. HRV was measured before and after a 12-week antidepressant treatment. We compared HRV measures between patient group and control group. We also tried to find correlation between HRV measures and depression rating scales. RESULTS: Fifty-seven participants were included (patient group: n鈥?鈥?1; control group: n鈥?鈥?6). The patient group showed a lower normalized high frequency (HF norm), a higher normalized low frequency (LF norm), and a higher LF/HF ratio than did the control group. After treatment, LF was significantly decreased within the patient group compared to baseline. Hamilton Depression Rating Scales and Children\'s Depression Inventory scores were positively correlated with LF norm and LF/HF ratio, and negatively correlated with HF norm, when included all participants in analysis LIMITATIONS: Sample size of this study was small to assess influences of confounding factors on HRV. And follow up period was relatively short to see impact of pharmacotherapy. CONCLUSION: An imbalance of the autonomic nervous system might be a meaningful feature of adolescent MDD, and HRV might represent a potential biological marker for pathophysiological changes in MDD.