Aim: Impaired autonomic function could be the mechanism for the development of cardiometabolic diseases in obesity. Hence, simple anthropometric measures of overall and central obesity could be screening markers for autonomic imbalance. We analysed the relationship between heart rate variability (HRV) parameters and obesity indicators. Methods: Sixty-three obese women underwent blood pressure, lipids and anthropometric measurements, body composition assessment, HOMA (homeostasis model assessment) index calculation and short-term HRV analysis. Results: The correlation between obesity indicators and HRV parameters was influenced by age. In the multiple regression model, sagittal abdominal diameter (SAD) was a significant negative predictor of lnLF/HF (logarithmically transformed ratio of low to high frequencies) and lnLFnorm, and positive predictor of HFnorm (normalized high frequencies); the significant relationship remained even after adjustment for age, HOMA, blood pressure, lipid profile, menopause, body mass index (BMI) and body fat percentage (FAT). Anterior forearm skinfold showed inverse association with HRV. Correlation between waist circumference and waist-to-height ratio (WHtR) with lnLF/HF, as well as between anterior thigh skinfold with lnLF/HF, LFnorm (normalised low frequencies) and HFnorm was lost after further adjustments. Conclusion: Among all anthropometric measures, SAD and anterior forearm skinfold thickness showed the highest predictive ability for HRV. Markers of lower sympathetic and higher cardiac parasympathetic activity corresponded with indicator of central obesity, while indicators of peripheral obesity showed completely opposite relationship with markers of cardiac autonomic activity.