BACKGROUND Considering the importance of Helicobacter pylori (H. pylori) eradication, this clinical trial was designed to prospectively evaluate the efficacy of levofloxacin-based, sequential therapy in comparison with quadruple therapy for eradicating H. pylori. METHODS Overall 156 patients with dyspepsia and H. pylori infection were included in this study and were randomly allocated to either 10-day sequential therapy group (group A) to receive pantoprazole (40 mg twice daily), amoxicillin (1 gr twice daily), levofloxacin (500 mg twice daily), and tinidazole (500 mg twice daily) (PALT) or 14-day quadruple therapy group (group B) to receive pantoprazole, clarithromycin, bismuth subcitrate, and amoxicillin (PABC). At the end of the study the eradication rate in each group was assessed by urea breath test (UBT). RESULTS Age range of the participants was 18-65 years (average 36.9 years) and 50% of them (78 patients) were men. 78 patients were allocated to group A and 78 patients to groupe B. After antibiotic therapy, all the patients received acid suppression therapy with Proton Pump Inhibitor (PPI) for 4 weeks and then the eradication rate was confirmed by UBT (Heli FAN plus 13C, Germany). Before performing UBT, all the participants were requested to halt consumption of PPI for at least 1 week. During the treatment there was not any major complication but in group A (sequential therapy), two patients complained of minor complications including musculoskeletal pain. None of the patients in group B had any complaint or side effect. The rate of H. pylori eradication in group A was 78.2% (61 patients) while this rate in group B was 83.3% (65 patients) with no significant difference between the two groups (p = 0.42). In subgroup analysis, the rate of eradication among men in group A and B were 76.9% and 89.7%, respectively (p = 0.22) while the eradication rate among women were 79.4% and 76.9%, respectively (p = 1.00). CONCLUSION It seems that levofloxacin base sequential therapy does not have any advantage in comparison with quadruple regimen and until finding any more effective short course therapy for H. Pylori eradication; we encourage quadruple regimen to be used as the first line therapy.