Background Clarithromycin-based triple therapy for Helicobacter pylori (H.pylori) eradication is not effective because of clarithromycin resistance.Berberine and allicin were shown to inhibit proliferation of H.pylori in vitro and to be potentially effective in patient.Whether berberine or allicin based triple regimen can replace clarithromycin as the first-line treatment is unknown.