The aim of this study was to assess the clinical outcome of two different durations of triple therapy in children with Helicobacter pylori infection. We established two treatment groups: 1) Short treatment, including 2 week of bismuth subcitrate, amoxycillin and metronidazole treatment (n = 21) and 2) Long treatment, which included the same therapy for two weeks plus bismuth subcitrate alone for two weeks more (n = 26). We found no difference between the short and long treatments. The infection remained in 14% and 19%, respectively. In both groups, we observed children (19%) with persistent abdominal pain in spite of Helicobacter pylori eradication and gastritis healing. We conclude that it is not necessary to prolong triple therapy more than 2 weeks in order to have therapeutic success.