Background: Obesity and anthropometric measurements predict more severe sleep-disordered breathing (SDB) in children, and are associated with cardiovascular risk factors in children without SDB. We aimed to investigate whether anthropometric measurements predicted autonomic control in children with SDB. We hypothesised that anthropometric measures would be significant predictors of decreased heart rate variability. Methods: Children (3-17 years) with SDB (n = 298) and non-snoring controls (n = 126) underwent polysomnography. BMI z-score, neck, waist and hip circumference were recorded. Heart rate variability, indicating autonomic control, was analysed during wake, non-rapid eye movement stages N1, N2 and N3, and rapid eye movement (REM) sleep. The determinants of heart rate variability (low-frequency power [LF], high-frequency power [HF] and LF/HF ratio) were analysed using multiple stepwise linear regression. Independent variables were age, neck, waist and hip circumference, neck-to-waist ratio, waist-to-hip ratio and waist-to-height ratio, obstructive apnoea hypopnoea index, arousal index and SpO2 nadir. Results: Waist and hip circumference, and waist-to-height ratio were significant negative determinants of both HF and LF power during wake, reflecting dampened autonomic control (LF: waist/height ratio, B =-1917 (95% CI:-3640,-194), p = 0.03; HF: hip circumference, B =-27, (-48,-7), p = 0.01), N1&2 (LF/HF: hip circumference, B = 0.01 (0.004, 0.024), p = 0.005) and N3 (LF: waist/height ratio, B =-2495, (-4005,-986), p = 0.001; HF, hip circumference, B =-54, (-102,-6), p = 0.03; LF/HF, waist circumference, B = 0.01, (0.004, 0.015), p = 0.002). Age was the strongest determinant of heart rate variability during wake and sleep. Conclusion: This study suggests that while age is a determinant of autonomic control in children with SDB, the strongest modifiable factor determining dampened autonomic control is increased central adiposity, as reflected in the waist and hip circumference and the waist-to-height ratio.