The results of previous studies suggest pathogenetic role of immune system in the development of schizophrenia. Examination of adolescent and young adult schizophrenic patients showed that the activity/ level of distinct parameters of innate and acquired immunity correlates with acuity and severity of pathological process in the brain. Presumably, evaluation of immune system characteristics in patients with childhood schizophrenia, concerning severity of their clinical symptoms, along with potential therapeutic aspect, may be the basis for early diagnosis of these conditions, and monitoring and prognosis of the further progression of the disease. The objective of our study was to compare clinical and immunological indices in children with schizophrenia to analyze the possibility of using these parameters for determination of the degree of activity of the pathological process. Sixty-two patients (39 boys and 23 girls) from 4 to 17 years of age with childhood schizophrenia were examined. Psychopathological and psychometric methods (PANSS and CGI-S scales) were used to assess mental state of the patients. Immunological parameters were determined in blood serum taken by fingerprick. Activity of leukocyte elastase (LE) and a1-proteinase inhibitor (a1-PI) was determined by spectrophotometric method. To determine the level of autoantibodies to S-100B and MBP, we used enzyme immunoassay. The study revealed activation of innate (by activity of LE and a1-PI) and acquired (by the level of autoantibodies to S-100B and MBP neuroantigens) immunity markers in blood serum of children with schizophrenia. Correlation analysis showed the significant positive correlation between complex evaluation of activation level of the immune system and severity of the patients’ state on the CGI-S scale (r = 0.64, p < 0.0001), as well as severity of negative symptoms according to the PANSS scale (r = 0.34, p = 0.0077). The revealed correlations suggest an opportunity for using immunological parameters (LE and a1-PI activity, and antibodies to neuroantigens), as the additional laboratory criteria for the assessment of clinical state in patients with childhood schizophrenia.