Background: The primary goal of this placebo-controlled study was to determine the effect of quadruple treatment with Saccharomyces boulardii or Lactobacillus reuteri on the eradication of Helicobacter pylori and side effects of the treatment.Results: This study was a double-blind, randomized, placebo-controlled trial. And, eradication of helicobacter pylori was reported comparing conventional anti-H. Pylori therapy versus conventional therapy supplemented with S. boulardii and L. reuteri DSMZ 17648. For this aim, a total of 156 patients were included in the current study; and patients positive for H. Pylori infection (n =156) were randomly assigned to 3 groups: 52 patients (Group P) received conventional quadruple therapy plus L. reuteri, 52 patients (Group S) received conventional quadruple therapy plus S. boulardii daily, for 2 weeks, and 52 patients were in the control group (Group C). At the end of the treatment period, all the subjects continued to take proton pump inhibitor (PPI) alone for 14 days, and then, no medication was given for 2 weeks again. During follow-up, gastrointestinal symptoms were assessed using an evaluation scale (Glasgow dyspepsia questionnaire (GDQ)), and adverse events were assessed at 7, 14, 21, and 28 days. As a result, eradication therapy was effective for 94.2% of subjects in Group S, 92.3% of subjects in Group P, and 86.5% of subjects in the control group, with no differences between treatment arms. In Group S, the chance of developing symptoms of nausea (OR=2.74), diarrhea (OR=3.01), headache (OR=10.51), abdominal pain (OR=3.21), and anxiety (OR=3.58) was significantly lower than in the control group (p<0.05).Conclusion: In general, our findings revealed that the use of probiotic supplements containing S. boulardii or Lactobacillus reuteri (DSMZ 17648 strain) improved the eradication rate of H. Pylori infection, but it was not statistically significant. Therefore, it is recommended to conduct future research with a larger sample size to investigate the effect of S. boulardii supplementation on eradicating H. pylori infection and reducing treatment side effects.Trial registration: IRCT20200106046021N1, this trial was registered on Jan 14, 2020.