Background/Aims: Similar autonomic innervation of the esophagus and left atrium with sympathovagal imbalance seems to explain the association between non-valvular atrial fibrillation (AF) and gastroesophageal reflux disease (GERD). We aimed to assess this association via parameters of heart rate variability in time (SDNN) and frequency (low-frequency (LF)/high-frequency (HF) ratio) domains by 24-hour electrocardiographic (ECG) Holter monitoring. Materials and Methods: One hundred thirty-five patients were prospectively included by a joint team consisting of a gastroenterologist and a cardiologist on the basis of the patients' complaints. A diagnosis of GERD was assessed by the gastroenterologist clinically. All patients also underwent upper gastrointestinal endoscopy. Results: The patients were included in two groups: 61 patients with GERD (group I) and 74 patients without GERD (group II), with demographic data of 41% male, age 61.5±9 years, and body mass index (BMI) 28.8±4 kg/m2 versus 46% male, age 58±9 years, and BMI 29±4 kg/m2 (all p>0.05). In groups I and II the percentages of patients with AF were 33% and 39%, respectively (p=0.52). Patients with GERD had a relative risk of AF of 1.17 (95% confidence interval [CI] 0.78-1.75; p=0.34). Heart rate variability in terms of the time-domain parameter (SDNN) was statistically significantly lower in the GERD group (97.6±13.7 ms versus 139.9±44.6 ms; p=0.001). The mean value of the frequency-domain parameter (LF/HF ratio) was also lower in the GERD group (0.75±0.17 ms versus 0.76±0.24 ms), but without statistical significance (p=0.930). Conclusion: Sympathovagal balance seems to be disrupted in patients with GERD, with dominance of the parasympathetic system and an increased risk of arrhythmias, although AF was not significantly more frequent in these patients.