INTRODUCTION: We investigated the association between autonomic nervous system (ANS) activity and symptoms of anxiety and depression for the first 2 years postpartum. METHODS: A total of 108 participants within 2 years postpartum underwent physiological measurements of ANS activity using the heart rate variability (HRV) power spectrum and self-reported questionnaires (14-item Hospital Anxiety and Depression Score). The cutoff points for anxiety and depressive symptom scores in this questionnaire were as follows: 7 or less, non-cases; 8-10, doubtful cases; 11 or more, definite cases. This study was conducted from 2012 to 2014 at University Hospital in Kyoto Prefectural University of Medicine and a nearby obstetrics and gynecology department clinic in Japan. RESULTS: Anxiety and depression non-cases accounted for 67.6% (n = 73) of subjects, anxiety non-cases and depression doubtful and definite cases 7.4% (n = 8), anxiety doubtful and definite cases and depression non-cases 8.3% (n = 9), and anxiety and depression doubtful and definite cases 16.7% (n = 18). Findings were similar for women with anxiety or depression, with total power (TP), low-frequency (LF) and high-frequency (HF) components of HRV among doubtful and definite cases significantly lower than among non-cases for both anxiety (p = 0.006, 0.034, 0.029, respectively) and depression (p = 0.001, 0.004, 0.007). Significant correlations were observed between TP, LF and HF and anxiety and depression scores (respective values for anxiety: rs = -0.331, p <0.001; rs = -0.286, p = 0.003; rs = -0.269, p = 0.005; and depression: rs = -0.389, rs = -0.353, rs = -0.337, all p <0.001). DISCUSSION: The present study demonstrated that mothers with anxiety or depressive symptoms had significantly lower HRV (HF, LF and TP) than those without.