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BACKGROUND: The standard triple therapy has lost a considerable proportion in it efficiency in treating Helicobacter pylori infection. As such several alternatives and adjuvants have been proposed. One the most promising modulation is the supplementation this therapy with probiotics. AIMS: This study aimed to investigate the efficiency of probiotic supplementation to traditional triple therapy in the eradication of Helicobacter pylori infection and alleviation of side effects. PATIENTS AND METHODS: This is a cross-sectional study included 310 consecutive patients newly diagnosed with gastritis or dyspepsia and infected with H. pylori. Patients were randomly divided into three groups based on treatment regimes. Group A: 100 patients received triple therapy consisting of omeprazole, amoxicillin and levofloxacin for two weeks. Group B: 100 patients received tinidazole, levofloxacin and omerprazole for two weeks. Group C: 110 patients received the second protocol plus the probiotic. All patients were reinvestigated four weeks after accomplished treatment by stool antigen test for H. pylori. RESULTS: The rate of successful H. pylori eradication was 77.74%. In multivariate analysis, each of age≤ 35 years (OR=0.51, 95%CI=0.28-0.93), being married (OR= 0.37, 95%CI=0.21-0.71), never smoker (OR= 0.55, 95%CI=0.32-0.95) and treatment regime with triple therapy supplemented probiotics (OR= 3.36, 95%CI=2.5-21.7) were significantly associated with increased the eradication rate. The overall incidence of side effect in group C was (7.27%) was lower than that B (19%) with significant difference, and group A (15%) with no significant difference. CONCLUSIONS: The use of probiotics as an additive for the standard triple therapy significantly increases the eradication of H. pylori and may reduce the incidence of side effect of the traditional therapy.