Hp-fast is a new rapid urease test (RUT) that has not been evaluated in children. The aim of the study was to prospectively compare the Hp-fast test to the CLOtest in children. Children with gastrointestinal symptoms who undergo diagnostic upper endoscopy were prospectively enrolled to the study. Antral gastric biopsies were evaluated for histology and for CLO-test and Hp-fast. Results were then compared to histology. Of the 94 children who participated, gastritis was found in 38 (40%), of whom 16 (42%) had associated H. pylori organisms. In two children, H. pylori organisms were identified without gastritis. The concordance between both RUT tests was 98%. A significant correlation was found between RUT results and histological factors or serology. The accuracy rate of both RUT increased significantly when different gold standards were utilized to detect Hp infection in children. The best correlation was found when histology and serology were considered as the gold standard for the diagnosis of H. pylori infection in children (sensitivity: 100% compared to 43-80% with other standards, respectively). In conclusion, the Hp-fast test result is comparable to CLOtest, but neither alone is sufficient to establish the diagnosis of Hp infection in children.