Objective: Microbiota has an important role in human metabolism, nutrition, immunity, and protection against colonization by pathogenic microorganisms. Radiation can harm the beneficial members of the gastrointestinal tract flora. Methods: Our study included 75 rural children aged 4-18 years, who lived in contaminated area exposed to natural environmental radiation with clinical symptoms of irritable bowel syndrome and 20 healthy urban participants aged 5-15 as control group. The intestinal bacterial microbiota was examined from stool samples. Findings: Our results indicated the population levels of microbiota such as Enterobacter, Enterococcus, Lactobacillus and Bifidbacterium in caecal contents in 61 subjects (81.3%) was significantly less than in control group. Conclusion: We investigated alternation of the intestinal microbiota affected by ionizing radiation in children with clinical symptoms of irritable bowel syndrome.