Background. The primary diagnosis of functional and organic disorders in the gastrointestinal system is always a big problem, especially in patients with systemic diseases caused by disorders of carbohydrate metabolism, which can manifest themselves as directly the development of somatic pathology, as well as dysfunction of the Autonomous nervous system The purpose is to study the structure of gastrointestinal diseases in patients with dysmetabolic disorders, in particular, with type 2 diabetes mellitus, the relationship of these disorders with indicators of autonomous regulation, and to evaluate the informativeness of some diagnostic methods in assessing the function of the stomach in these patients. Material and methods. The study involved two stages. On the ground were examined 312 patients with impaired carbohydrate metabolism, with emphasis on the structure of comorbid pathology. The second phase was conducted in-depth survey of 49 patients to assess the state of processes of autonomic regulation and the functional state of the stomach. During the examination, special methods were used, such as intragastric pH-metry, gastroscintigraphy, and assessment of heart rate variability. Results. The prevalence of diseases of the gastrointestinal tract in patients with impaired carbohydrate metabolism was very high and depended on the duration of the disease (more than 10 years in 100% of patients) and the severity of dysmetabolic disorders - in 91.5% of patients with unsatisfactory control of metabolic processes and in 25.3% of cases, if the disorders of carbohydrate metabolism were well controlled. The risk of developing concomitant pathology of digestive organs was higher in patients with multiple complications (RR=1,214, p<0.01, overweight (OR=5.37; p<0.001). Patients with disturbance of the autonomous regulation were more frequent hypersympathictonу that pursued disturbances of the acid-forming and motor-evacuation function. Conclusion. In the pathogenesis of comorbid diseases that combine vomiting of the gastrointestinal tract and dysmetabolic disorders (disturbance of carbohydrate metabolism), the development of Autonomous neuropathy is important, which is simultaneously the cause of the progression of comorbid pathology and its consequence. The presence of Autonomous neuropathy makes it difficult to diagnose the disease and should be taken into account in the complex therapy of comorbid diseases. © 2020 Global Media Tekhnologii. All rights reserved.