The aim is to compare high-dose rabeprazole and amoxicillin containing modified dual therapy (MDT) with bismuth subcitrate containing standard quadruple therapy (SQT) as the first-line Helicobacter pylori eradication treatment in terms of efficacy, safety, and adherence to treatment. A total of 200 consecutive patients diagnosed endoscopically with nonulcer dyspepsia with H. pylori infection were randomly assigned into 2 groups, 1 treated with amoxicillin 750 mg thrice daily plus rabeprazole 20 mg thrice daily (MDT group) or rabeprazole 20 mg b.i.d., bismuth subcitrate 120 mg q.i.d., tetracycline 500 mg q.i.d., metronidazole 500 mg t.i.d. (SQT group). Overall, 196 patients (98 in the MDT group and 98 in the SQT group) completed the study. H. pylori eradication was achieved in 84.7% of patients in the MDT group by intention to treat analysis and 84.9% by per-protocol analysis, which were comparable with SQT group (87.8% and 88.8%, respectively). Adverse events including nausea (P = 0.03), dysgeusia (P < 0.001), diarrhea (P = 0.001), black colored stool (P < 0.001), headache (P = 0.01), and abdominal pain (P = 0.05) were significantly higher in SQT group. The MDT is an efficient and safe treatment choice that could be recommended in the first-line eradication treatment of H. pylori.