Abstract Background Sex-specific differences in cardiac autonomic tone have not been thoroughly investigated in patients with atrial fibrillation (AF) but may play a relevant role. Purpose We aimed to investigate cardiac autonomic function of female compared to male AF patients by means of short-term heart rate variability (HRV) analysis. Methods In this cross-sectional analysis, we enrolled 1150 patients from the Swiss-AF cohort study with 5-minute resting ECG recordings in sinus rhythm. We calculated the following HRV parameters: HRV triangular index (HRVI), standard deviation of NN intervals (SDNN), root mean square of successive differences, mean heart rate, power in the high frequency and low frequency range. We fitted linear regression models to analyze the association between gender and HRV variables adjusted for age, intake of betablockers, hypertension, diabetes and heart failure. Results 361 patients (29%) were female (mean age 72.9±7.8 years), 789 (68.6%) were male (mean age 69.8±8.5 years). In the multivariable adjusted models, female sex was associated with significantly lower values of HRVI (β = -0.74; 95% CI -1.44- -0 04, p=0.039) and SDNN (β = 8.95; 95% CI 0.162-17.7, p=0.046). This association persisted in all three age tertiles (<68 years, 68-75 years and ≥ 75 years of age). Conclusions In an elderly AF cohort, female sex is associated with reduced global autonomic activity. Whether this is associated with an adverse prognosis has to be investigated.