We showed the data on clinical efficiency of low doses of antibodies to brain-specific protein S100 in the complex therapy of schoolchildren with painful variant of functional dyspepsia syndrome. Significant positive effects of the substance on the dynamics of epigastric pain, in particular, its duration, were found. The maximum clinical effect was observed in children with emotional disorders (~1/3 of all examined children). Along with significant decrease in frequency appearance and duration of pain syndrome, the substance also normalized emotional state and improved attention concentration in children.