The aim of the clinical research was to study the efficacy of Saccharomyces boulardii in treatment of patients with Inflammatory Bowel Diseases. Results of investigation demonstrate more rapid regression of intestinal dyspepsia symptoms, decreasing clinical activity of IBD and improvement of intestinal microbiota composition in IBD patients have been treated by Saccharomyces boulardii. Lyophilized Saccharomyces boulardii are compatible with medical agents of the standard IBD therapy and have high level of safety.