STUDY OBJECTIVE: As resistance of Helicobacter pylori to standard first-line therapy is increasing globally, alternative treatment regimens, such as a fluoroquinolone-based sequential regimen, have been explored. The objective of this meta-analysis was to compare the efficacy of fluoroquinolone-based sequential therapy with standard first-line treatment for H. pylori infection. DESIGN: Meta-analysis of six randomized controlled trials. PATIENTS: A total of 738 H. pylori-infected, treatment-naive adults who received fluoroquinolone-based sequential therapy (5-7 days of a proton pump inhibitor [PPI] and amoxicillin therapy followed by 5-7 days of a PPI, a fluoroquinolone, and metronidazole or tinidazole or furazolidone therapy) and 733 H. pylori-infected, treatment-naive adults who received guideline-recommended, first-line therapy with standard triple therapy (7-14 days of a PPI plus amoxicillin and clarithromycin) or standard sequential therapy (5 days of a PPI plus amoxicillin, followed by an additional 5 days of triple therapy consisting of a PPI, clarithromycin, and metronidazole or tinidazole). MEASUREMENTS AND MAIN RESULTS: A systematic literature search of the MEDLINE, PubMed, and Cochrane Central Register of Controlled Trials databases (from inception through January 2015) was conducted to identify randomized controlled trials that compared fluoroquinolone-based sequential therapy with guideline-recommended, first-line treatment regimens in H. pylori-infected, treatment-naive adults. All selected trials confirmed H. pylori infection prior to treatment as well as post-treatment eradication. A meta-analysis was performed by using Review Manager 5.2. Treatment effect was determined with a random-effects model by using the Mantel-Haenszel method and was reported as a risk ratio (RR) with 95% confidence interval (CI). In the six randomized controlled trials that met the inclusion criteria, 648 (87.8%) of 738 patients receiving fluoroquinolone-based sequential therapy and 521 (71.1%) of 733 patients receiving standard regimens achieved eradication (RR 1.21, 95% CI 1.09-1.35). The frequencies of adverse effects that were reported in three of the trials were comparable for all treatments (RR 0.99, 95% CI 0.76-1.29). In addition, no statistically significant difference was noted in the number of patients who experienced adverse effects that prompted discontinuation of therapy (RR 1.03, 95% CI 0.34-3.09). The H. pylori eradication rate appeared similar among the six trials with respect to duration of therapy and daily dose of the fluoroquinolone. CONCLUSION: Fluoroquinolone-based sequential therapy is a reasonable treatment alternative to first-line eradication therapy for treatment of H. pylori.