Introduction: In many cases of aethelogy the gut microflore of gastrointestinal tract change by quantity, quality and structure then mainly occurred propagation and increase informal microflore. And that is the cause of aggravation of dysbacteriosis. In dysbacterios species and number of gut microflore of gastrointestinal tract increasing year by year and information of prior unsearched microflores are being increased.Especially, changing level in gut microbiota after Helicobacter pylori eradication therapy of chronic gastro duodenal disorder has not studied yet in the field, pediatric gastroenterology in Mongolia.Objective: To determine the effects on normal gastrointestinal microbiota after eradication therapy of Helicobacter pylori for chronic gastro duodenal disorder.Materials and Methods: A prospective cohort study of 50 patients, average age 12.82±2.9, during two years period from 2009-2010, evaluating the gut microbiota after Helicobacter pylori eradication therapy of chronic gastro duodenal disorder in Gastroenterology Unit, Maternal and Child Research Health Center.Results: Of the 50 patients there were 16 (32%) with peptic ulcer and 34 (68%) chronic gastroduodenitis due to Helicobacter pylori infection. The triple treatments were used in 34 cases (68%), the quartile treatment used in 16 cases (32%) and the probiotic combination therapy used in 27 cases (54%). After Helicobacter pylori eradication therapy, the H pylori serology test was positive in 9 cases (18%) and negative in 41 cases (82%). Before Helicobacter pylori eradication therapy, 45 cases (90%) had abnormal gut microbiota, 5 cases (10%) had normal gut microbiota. After eradication therapy with a probiotic, 19 cases (70%) had normal gut microbiota.Conclusion: After Helicobacter pylori eradication therapy there was an alteration in normal gut microbiota. The probiotic combination therapy was more effective in establishing normal gut microbiota than the non-probiotic combination therapy.