The aim of the investigation was to study the peculiarities of autonomic regulation using spectral analysis of heart rate variability for differential diagnostics of peptic ulcer and idiopathic duodenal ulcer.Materials and Methods. A stress level was assessed by vagosympathetic balance rate. low-high frequency ratio in a frequency spectrum of heart rate was used as a marker of vagosympathetic balance of stress. Endoscopic findings were compared with Helicobacter pylori test, and autonomic status was studied using spectral analysis of heart rate variability.Results. we found significant differences in low/high frequency ratio in the spectrum of heart rate of patients with Hp-positive and Hpnegative duodenal ulcers. The result proved stress nature of idiopathic ulcers. Idiopathic ulcers are characterized by significant increase of lf/Hf that can serve as a differential diagnostic criterion for different types of duodenal ulcers.Conclusion. Spectral analysis of heart rate variability can be used in differential diagnostics of peptic ulcers and idiopathic ulcers.