The prevalence of chronic kidney disease (CKD) in the population exceeds 13%. A high level of comorbidity of CKD and gastrointestinal tract (GIT) pathology is noted, which is induced by metabolic disorders, the dosing of a number of drugs damaging epithelium and parenchymatous organs of the GIT, reproduction of pathogenic and opportunistic pathogenic microflora under the conditions of decreased local and systemic immunity. Damage of GIT’s organs in patients with CKD is associated with the development of a systemic inflammatory process leading to impaired synthesis of tight conjunction proteins and increased permeability of the epithelial barrier. The development of secondary GIT’s pathology against the presence of CKD has the opposite effect associated with the increase of CKD progression rate, limitation of the conducted treatment’s possibility and development of severe complications. Over the past decade, the association of two metabolically associated diseases — non-alcoholic fatty liver disease and CKD — has come to be regarded by specialists as a major public health problem worldwide due to high morbidity level and adverse outcome. The study objective is to analyze the current data on the general pathogenetic mechanisms of comirbidity of the digestive organs and CKD in terms of evaluation of diagnostic and prognostic aspects depending on the development stage of the pathological process.