Atopic dermatitis (AD) is a chronic recurrent skin disease in individuals with a hereditary predisposition to atopy. The chief complaint in patients with AD is itching. It is known that during stress itching increases due to activation of neuropeptides and development of neurogenic skin inflammation. The decrease in intestinal microbiome variety correlates with the disease severity, especially in skin with AD changes. The interaction of microbiota and central analyzers in the brain is carried out with the participation of neurochemical substances (acetylcholine, histamine, catecholamines, corticotropin, etc.). At the same time, the association between the variation in the neurotransmitters content and the intestinal microbiome and their impact on the efficacy of the AD therapy is little studied. In the present study, based on psychodiagnostic and clinical laboratory examination of 168 patients with AD, the serotonin concentration in the blood serum increased to 102.4 ng/ml during the acute period of AD with a simultaneous increase in the level of opportunistic microbiota in stool assay. In addition, there has been a relevant increase in serotonin level during the acute AD compared to the group of healthy participants, where this indicator was 67.1 ng/ml. Species composition of microbiota in patients with acute AD varied greatly and exceeded the values in control group. The efficacy of comprehensive therapy, including correction of neurohumoral disorders and intestinal microbiota with the use of drug therapy, has been proved. The efficacy of comprehensive therapy suggests that it should be included in the standard treatment of patients with AD.