Study Objective. To determine the factors that may influence Helicobacter pylori eradication in patients receiving omeprazole‐amoxicillin dual therapy. Design. Prospective, randomized study. Setting. University‐affiliated hospital in Taiwan. Patients. A total of 128 adults (age range 20–75 yrs) with H. pylori‐positive duodenal ulcer were enrolled; 121 completed the final evaluation. Intervention. Patients were randomly assigned to one of four omeprazole‐amoxicillin treatment groups, with each treatment administered for 2 weeks: O2A2 group (33 patients)—omeprazole 20 mg twice/day plus amoxicillin 500 mg 4 times/day; O2A1 group (32 patients)—omeprazole 20 mg twice/day plus amoxicillin 250 mg 4 times/day; O1A2 group (32 patients)—omeprazole 20 mg once/day plus amoxicillin 500 mg 4 times/day; and O1A1 group (31 patients)—omeprazole 20 mg once/day plus amoxicillin 250 mg 4 times/day Measurements and Main Results. Data were collected on H. pylori status, histologic parameters, antibiotic resistance, intragastric pH, cytochrome P450 (CYP) 2C19 genotype, and adverse reactions. The intent‐to‐treat cure rates (95% confidence interval CI) in groups O2A2, O2A1, O1A2, and O1A1 were 76% (95% CI 59–87%), 72% (95% CI 54–84%), 50% (95% CI 34–66%) and 52% (95% CI 35–68%), respectively. Eradication of H pylori infection was statistically significantly dependent on omeprazole dosage, CYP2C19 genotype, age, gastritis status, and H. pylori density. All CYP2C19 poor metabolizers were cured, whereas the H pylori cure rate in CYP2C19 extensive metabolizers varied from 44–76% in the different treatment groups. Eradication of H. pylori was favored in the omeprazole higher dose groups versus the lower dose groups (79% vs 53%, p=0.004). No secondary antibiotic resistance was found. Thirty‐seven (95%) of 39 patients who failed with the initial treatment were cured by subsequent antibiotic susceptibility‐driven proton pump inhibitor‐based triple therapy. Conclusion. Provided a maintenance dose of amoxicillin is given every 6 hours, eradication of H pylori infection was significantly dependent on omeprazole dosage, CYP2C19 genotype, age, gastritis status, and H pylori density.