Autism is a pressing global problem in a number of medical and related scientific disciplines. For autism, a polysystemic feature is typical, and neurological changes are usually accompanied by somatic ones, most often affecting the intestine, pancreas, and often lungs, pelvic organs, kidneys, adrenal glands and other organs. It is not surprising that the mortality from somatic causes in such children exceeds the mortality of healthy children of the same age groups by 3–10 or more times (depending on the severity of autism). Many studies report a high prevalence of gastrointestinal symptoms in autistic people. The most common of these is chronic constipation (22% on average). The functional interaction of the gastrointestinal tract and the central nervous system is due to the presence of various connections and includes the autonomic nervous, immune and neuroendocrine systems. Of particular importance in gastrointestinal disorders and the pathogenesis of autism is the intestinal microbiota, a complex bacterial community located in the gastrointestinal tract. Under the influence of external and internal factors, the microbiota changes the permeability of the intestinal and blood-brain barriers, and the metabolites produced by the altered microbiota can enter the bloodstream and the central nervous system, disrupting its functioning. It was proven that there are pronounced differences between the intestinal microbiota of healthy children and autistic children, and directed individual correction often leads to normalization or significant improvement in social and communicative behavior and other deviations typical of children with autism. Thus, violations in the somatic sphere can increase the severity of the clinical presentation of autism, causing various behavioral and communication disorders. Identification of the spectrum of these disorders, as well as the study of the mechanisms of their development and interrelationship, is an urgent problem, the solution of which may be important for determining the tactics of complex therapy of patients with autism spectrum disorders.