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Helicobacter pylori (H pylori) is a common gastric pathogen which is associated with chronic gastritis, peptic ulcer, and gastric cancer. It has worldwide distribution with higher incidence in developing countries. Gemifloxacin is a fluoroquinolone antibiotic with documented in vitro activity against H pylori. Considering that there is no clinical data to verify gemifloxacin efficacy in H pylori eradication, this pilot clinical trial was designed.This prospective pilot study was performed during February 2014 to February 2015. A regimen of gemifloxacin (320 mg single dose) plus twice daily doses of amoxicillin1g, bismuth 240 mg, and omeprazole 20 mg for 14 days were prescribed for H pylori infected patients in whom a first-line standard quadruple therapy (clarithromycin–amoxicillin–bismuth–omeprazole) had failed. To confirm H pylori eradication a 13C-urea breath test was performed 4 weeks after treatment.Compliance and incidence of adverse effects were evaluated by questionnaires.A total of 120 patients were enrolled consecutively; out of which 106 patients achieved H pylori eradication; per-protocol and intention-to-treat eradication rates were 91.4% (95% CI: 85.5–97.6) and 88.3% (95% CI: 75.4–92.4) respectively. Three patients (2.5%) failed to take at least 80% of the drugs and excluded from the final analysis. Adverse effects were reported in 42% of patients, most commonly including nausea (15%) and diarrhea (13.3%), which was intense in 1 patient and led to the discontinuation of treatment. In total, 96.7% (116/120) of the patients took the medications correctly.This study revealed that gemifloxacin-containing quadruple therapy provides high H pylori eradication rate (≥90% PP cure rate), and this agent can be included in the list of second-line H pylori therapeutic regimens.