Helicobacter pylori-associated infection is extremely common in Iran, as in other developing countries, but few data exist on the susceptibility of H. pylori to antimicrobials commonly used in the eradication schedules in this country. This study was performed to determine the resistance rate to six antimicrobial agents used in the treatment of H. pylori infection in dyspeptic Iranian children and to recommend an updated anti-H. pylori treatment regimen to use in children. All H. pylori isolated from children who were undergoing gastroscopy were prospectively collected and subcultured to yield their susceptibility to six antimicrobial agents, by E test and disk diffusion methods. Demographic data and presenting symptoms were also collected. A prospective study was carried out from January 2003 to January 2005 with 100 strains of H. pylori isolated from children (40 girls and 60 boys; age range, 1.5 to 16 years [mean, 9.22 +/- 3.25 years]); the strains had been successfully subcultured to yield antimicrobial sensitivity. Overall the H. pylori resistance rate was 95% to metronidazole, 59% to amoxicillin, 16% to clarithromycin, 9% to furazolidone, 7% to ciprofloxacin, and 5% to tetracycline. The most common presenting symptom was abdominal pain. There were no statistically significant differences in antimicrobial resistance rates related to age, sex, or clinical presentation. In the Iranian children, the prevalence of H. pylori resistance was very high to metronidazole and amoxicillin, moderate to clarithromycin, and low to ciprofloxacin and tetracycline.