Background/aims: Sequential therapy is one of the recent answers given to the problem of increasing antibiotic resistance and decreasing eradication rates of Helicobacter pylori infection. The aim of this study is to compare the ornidazole-based sequential therapy with the standard triple therapy in Helicobacter pylori eradication. Materials and Methods: Children aged 4-18 years diagnosed with Helicobacter pylori infection based on histology and at least one of C-13 urea breath test and rapid urease test positivity were included in the study. Children were randomized to standard triple therapy with amoxicillin, clarithromycin, and lansoprazole for 14 days and sequential therapy with amoxicillin and lansoprazole for the first 5 days and clarithromycin, ornidazole and lansoprazole for another 5 days in 2:3 randomization. At the end of the treatment, families were contacted by phone, and side effects of and the compliance to the treatment were noted. Patients were requested to do C-13 urea breath test 6-8 weeks after the treatment. Results: Sixty-one children were included for the final analysis. Per-protocol eradication rates were 48.6% for sequential therapy group and 54.2% for standard triple therapy group. Intention to treat eradication rates were 40.9% and 46.0%, respectively. There were no differences between eradication rates in the two study groups. Side effect rates were also similar between the two groups. Conclusions: Ornidazole-based sequential therapy did not show any superiority compared to the standard triple treatment in children with Helicobacter pylori infection.