The review presents up-to-date information on the pathogenesis of disorders of the intestinal microbiotope and the relationship of these disorders with the use of medications traditionally prescribed in treatment regimens for various diseases, presents the main aspects of drug-microbial interactions, highlights the issues of correction of iatrogenic intestinal dysbiosis. One of the main exogenous factors in the development of intestinal dysbiosis at the present time, of course, can be considered drug therapy. The extremely widespread and often uncontrolled use of antibacterial drugs, nonsteroidal anti-inflammatory drugs, laxatives, drugs for the correction of carbohydrate metabolism, proton pump inhibitors, glucocorticosteroids, antidepressants, cytostatic drugs to a greater or lesser extent has a negative effect on the human microbiotope. On the one hand, the microbiota is a drug target, on the other hand, the gut microbiota itself can have both direct and indirect effects on the metabolism of drugs. The potential of the influence of microorganisms on the absorption, distribution, and metabolism of drugs deserves increased attention and detailed study. At the same time, the issues of prevention and correction of intestinal microbiota disorders against the background of taking various medications deserve even more attention from doctors of various profiles with the mandatory inclusion of drugs that harmonize the intestinal microbiotope in the treatment regimens of the underlying disease.