Endogenous intoxication syndrome is one of the leading syndromes in high urinary system infection activity in children. The study of clinical and laboratory manifestations of endogenous intoxication syndrome with the aim of optimizing its methods of therapy is topical. The examination was conducted in 52 children aged 3–7 years, including 22 children with active forms of pyelonephritis and 30 almost healthy children (control group). Endogenous intoxication syndrome was determined by clinical signs and by the level of leukocyte index of intoxication and medium-sized molecular peptides in blood plasma. Statistical analysis was carried out on the basis of Student’s t-test (p<0.05), the frequency of symptom occurrence (q) in relation to the totality in the group taken for 1 and the coefficients (Q) of the ratio of the comparable indicators in groups. In the control group, the leukocyte intoxication index did not exceed 1.0, the average molecular peptides— 0.24 conditional units. Most patients (q-0.73) had a moderately severe course, expressed symptoms of intoxication, pain abdominal syndrome (q-0.73), dysuria (q-0.73), high temperature (q-0.73). In complex therapy, prebiotic (complex fructoolygosaccharides, inulin and maltodextrin) was prescribed in age dosage for three weeks. Detoxification therapy contributed, first of all, to the positive dynamics of clinical manifestations of the intoxication syndrome. During the first two days, the temperature reaction decreased; on the 4-5th day, the general condition improved, other symptoms of intoxication disappeared; highly reliable (p<0.001) positive changes in the studied indicators were found within 3 weeks. They were characterized by the normalization of the level of leukocyte index of intoxication and medium-sized molecular peptides, which justifies the use of prebiotic products in the complex therapy of urinary system infection in children.