We investigated the extent to which obesity could identify autonomic dysfunction of heart control in a cross-sectional study with 65 women (aged 18-45 years), categorized as eutrophic, overweight or obese. We collected anthropometric measures and measures of heart rate variability (HRV) between March 2015 and March 2017. Low frequency in normalized units (LF((nu))) over 46 was considered a marker of autonomic imbalance and high frequency in normalized units (HF((nu))) below 38 a marker of depressed vagal modulation. Overweight (mean difference MDeltaHF((nu)) = -13.11 [95% confidence interval (CI) of difference, -25.88, -0.34], Hedges\'s g = 0.65, common language effect size (CL) = 68.1%) and obese (MDeltaHF((nu)) = -21.22 [95% CI, -31.89, -10.55], Hedges\'s g = 1.17, CL = 79.2%) women presented depressed vagal modulation compared to eutrophic women. Autonomic imbalance increased as body mass index increased (eutrophic-to-overweight MDeltaLF((nu)) = 13.06 [95% CI, 1.65, 24.47], g = 0.65, CL = 67.9%, and overweight-to-obese MDeltaLF((nu)) = 21.07 [95% CI, 10.32, 31.82], g = 1.15, CL 78.9%). The odds ratio for depressed HF((nu)) among overweight women was 2.36 (95% CI 0.77, 7.29) and 2.18 among obese women (95% CI 0.79, 5.99), as well as 9.17 (95% CI 2.62, 32.04) and 17.39 for increased LF((nu)) (95% CI 2.13, 141.76), respectively. The parasympathetic activity is diminished and autonomic imbalance of the cardiac control increased with increasing BMI categories.