ABSTRACT: Understanding relationships between specific measures of adiposity and heart rate variability (HRV) allows for better understanding obesity as a risk factor for cardiovascular and autonomic dysfunction. We sought to examine associations between specific adiposity depots and cardiovascular autonomic function assessed via HRV among children and adolescents. We performed a secondary cross-sectional analysis of a previously completed study of 8-17-year-olds (n = 325; 12.4 ± 2.7 years). Adiposity was assessed via dual x-ray absorptiometry. Resting HRV measures included root mean square of successive differences (RMSSD), percentage of successive normal-to-normal intervals differing by more than 50 ms (pNN50), low frequency power (LF), high frequency power (HF), and low frequency-to-high frequency ratio (LF:HF). Associations between adiposity and HRV were evaluated using linear regression modeling, adjusting for sex and Tanner stage. RMSSD and pNN50 were both negatively associated with total fat (β = - 0.558, p = 0.004; β = - 0.178, p = 0.034), percent body fat (β = - 0.790, p = 0.007; β = - 0.296, p = 0.019), trunk fat (β = - 1.024, p = 0.004; β = - 0.344, p = 0.022), android fat (β = - 0.005, p = 0.006; β = - 0.002, p = 0.028), gynoid fat (β = - 0.003, p = 0.005; β = - 0.001, p = 0.034), visceral adipose tissue (β = - 0.013, p = 0.016; β = - 0.005, p = 0.038) and subcutaneous abdominal adipose tissue (β = - 0.007, p = 0.004; β = - 0.003, p = 0.017). RMSSD was negatively associated with appendicular fat (β = - 1.152, p = 0.008). Visceral adipose tissue was associated positively with LF and LF: HF (β = 0.004, p = 0.028; β = 0.019, p = 0.033) and negatively with HF (β = - 0.004, p = 0.028). We found that excess total and regional adiposity may have negative effects on cardiovascular autonomic nervous system function in a large cohort of children and adolescents. Longitudinal studies are needed to confirm and determine how these relationships change over time.