The prevalence of peptic ulcer disease in hemodialysis dependent patients is higher than the general population. These patients are also more prone to upper gastrointestinal bleeding. The aim of this study was to compare the effects of a standard triple therapy with a sequential therapy on Helicobacter pylori eradication in azotemic and hemodialysis patients. Forty nine hemodialysis and azotemic patients, naïve to H. pylori treatment, were randomized into two groups to receive either standard triple therapy (pantoprazole 40 mg, amoxicillin 500 mg and clarithromycin 250 mg twice a day for 14 days) or a sequential therapy (pantoprazole 40 mg for 10 days, amoxicillin 500 mg twice a day for the first 5 days and clarithromycin 250 mg + tinidazole 500 mg twice a day just during the second 5 days). H. pylori eradication was evaluated by fecal H. pylori antigen assessment 8 weeks after the treatment. Of 49 patients, 45 patients (21 in triple therapy group and 24 in the sequential group) completed the study. Based on intention to treat analysis, H. pylori eradication rates were 66.7% (95% confidence interval CI: 47.8-85.5%) in standard triple therapy group and 84% (95% CI: 69.6-98.3%) in sequential therapy group (P = 0.34). Per-protocol (PP) eradication rates were (95% CI: 76.2%. 6-89.3%) 54 and 87.5% (95% CI: 68.8-95.5%), respectively (P = 0.32). According to Maastricht III consensus report, the results of our study showed that sequential therapy might be a better choice compared with the standard triple therapy in azotemic and hemodialysis patients Iran. We propose to assess the effects of shorter-duration sequential therapy (less than 10 days) for H. pylori eradication.