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The purpose of study is to establish features of autoimmune reaction of children with Crohn's disease. The sampling included 62 patients aged from 2 to 17 years with diagnosis of Crohn's disease. The evaluation was carried out concerning concentration in blood serum of immunoglobulins IgA, IgM, IgG, IgЕ, antibodies to Saccharomyces cerevisiae (ASCA) classes IgA, IgG и IgЕ, antibodies to Candida albicans classes IgA, IgM, IgG и IgЕ, anti-neutrophilic cytoplasmic antibodies (ANCA) to myeloperoxidase (MPO), to proteinase 3 (PR3), anti-nuclear antibodies (ANA), antibodies to DNAds, DNAss (to double-helical and single-stranded DNA), antibodies to antigens of small and large intestines, pancreas, circulating immune complexes. The hyperimmunoglobulinemia was diagnosed in 47 (75.8%) out of 62 patients with Crohn's disease. The increased level of IgM in blood was detected in 29 patients (46.8%). The hyperimmunoglobulinemia У was established in 19 (30.6%) out of 62 children. The hypoimmunoglobulinemia was detected in 22 (35.5%) of patients and in 17 (77.3%) out of them the disimmunoglobulinemia type IV (isolated decreasing of concentration of IgA). The evaluation of rate of occurrence of specifc antibodies in blood serum demonstrated that in patients most frequently was detected presence of specifc IgE to Saccharomyces cerevisiae (70.9%). The increased level of ASCA (IgA, IgG) was detected in 22 (35.5%) patients. The concentration of antibodies to DNAds, DNAss in blood exceeded standard value in 4.8% and 16.1% patients correspondingly. The increased level of circulating immune complex was established in 20 (32.3%) patients. The concentration of ANA corresponded to standard values in all 62 (100%) patients. The evaluation of results of correlation analysis established a strong positive correlation of concentration in blood of antibodies to antigens of small and large intestines; average positive correlation of level of antibodies to antigens of small intestine and IgM, ANCA PR3, ASCA IgE, antibodies to Candida albicans classes IgM, IgG, IgE, antibodies to antigens of pancreas; average degree of positive correlation between concentration of antibodies to antigens of large intestine and IgA, IgM, circulating immune complex, ANCA PR3, DNAss, ASCA IgE, antibodies to antigens of pancreas; strong positive correlation between concentrations of IgA to Candida albicans and ANA. The detection of auto-to antibodies Saccharomyces cerevisiae, Candida albicans, ANCA, antigens of small and large intestines, pancreas and expressed degree of correlation of many indices of autoimmune reaction indicate to intensity of immune pathological process under Crohn's disease. Under Crohn's disease, the formation of antibodies to ASCA is a prognostically unfavorable sign. The immune diagnostic under Crohn's disease is necessary for evaluating severity of course of disease, differential diagnostic, establishment of prognosis and selection of individual immune correcting therapy.