In 57 patients with ulcer disease the spectral analysis of the heart rhythm variability (HRV) was conducted for estimation of the vegetative nervous system (VNS) state. In 66.7% of patients there was noted prevalence of the parasympathetic part of VNS tone, in 14.0% - sympathetic one. Dystonic activity of various parts of VNS had accompanied by raising of definite mediators (markers) of VNS: acetylcholine (r = 0.75), adrenaline and noradrenaline (r = 0.25), complicated course of ulcer disease. Sympathicotonia was associated with ulcerative hemorrhage (r = 0.5), vagotonia with perforation of the ulcer (r = 0.75). So, choosing the surgical intervention volume in patients with the ulcer disease it is expedient to apply the method of spectral analysis of HRV for estimation of the VNS state.