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The efficacy of a gut microbiota control was investigated for patients with atopic asthma. 45 patients with atopic asthma were included in the study. The results of our clinical and lab tests, pulmonary function tests and the lactulose hydrogen breath tests have been presented to evaluate small intestine bacterial overgrowth (SIBO). Under the standard SIBO’s therapy (long-acting beta-agonists, inhaled glucocorticoids), the first group (15 patients) had being tested with Rifaximin for the SIBO therapy during 7 days. The second group (15 patients) had been tested with Rifaximin and with a succeeding probiotics therapy for three months (B. bifidum, B. longum, B. infantis, L. rhamnosus). SIBO was diagnosed for 30 (67%) patients. We have detected a higher IgE level (P<0.01), a higher eosinophils level (P<0.001) in sputum and more significant decrease of FEV1 (P<0.01) in SIBO(+). The IgE level in patients was decreased (P<0.01) after the complex SIBO therapy both for the Rifaximin therapy group (P<0.05) and for the Rifaximin + Probiotic therapy group (P<0.05). A dramatic decrease of the IgE level (P<0.05) had been induced by probiotics and it was confirmed by the control testing results with a high statistical accuracy for the observed groups of patients. We did not detect any changes for the patients without SIBO (P=0.46), those who had been treated with a standard therapy. A decrease in the number of patient hospitalization was defined by the treatment with probiotics after SIBO therapy (P<0.05). So, SIBO is a significant factor aggravating the atopic asthma in patients. The gut microflora correction with probiotics therapy has been accompanied by a statistical reliability improvement for the immune response and spirometry, as well as by a decrease in the number of hospitalizations for these patients during the year.