Neuronal structure was studied during a year after the truncal subdiaphragmatic two-side vagotomy in nuclei of vagal nerves and oblongated medulla. Jacobson nuclei in the spinal cord lateral cornua and stomach and intestinal nerve plexuses. Dynamics of structural changes in nervous system different regions after vagotomy was shown. In intramural nerve ganglionic structure repairs on late post operative terms, while vagal nerve nuclei in the oblongated medulla retain significant changes, one of which is the sharp decrease of neuron number a year after vagotomy. Compensation of Jacobson nuclei similar to nucl. intermediolateralis was taken into consideration. So vagotomy is a surgical intervention into nervous system and into endocrine system associated with it.