AIM: To investigate the diagnostic value of gene chip test for detection of Helicobacter pylori (H.pylori) infection in children, and to assess the relationship between H.pylori virulence factors and the severity of gastroduodenal lesions. METHODS: A total of 30 children with symptoms of the digestive system, such as abdominal pain, vomiting, melena and hematemesis, underwent the 13C breath test at Beijing Children's Hospital from October 2007 to April 2008. A gene chip test was then performed for positive cases. The sensitivity and specificity of the gene chip test were analyzed. Gastroscopy was performed in patients diagnosed with H.pylori infection by both of the above methods. The pathological changes in gastroduodenal lesions were examined by gastroscopy to assess the relationship between H.pylori virulence factors and the severity of H.pylori. The results were analyzed by the Kappa test. RESULTS: The gene chip test has a sensitivity of 93.7%, a specificity of 60%, and a rate of missed diagnosis of 6.3%. The coincidence rate between the 13C breath test and gene chip test is 89.1%, showing a good consistency. H.pylori CagA antibody was detected in 96.6% (29/30) of the patients, while the detection rate of VacA antibody is 3.3%. H.pylori carrying CagA may have a stronger pathogenicity. The presence of CagA antibody was often related with gastritis, peptic ulcer and Henoch-Schonlein syndrome (abdominal type), while the presence of VacA antibody predicted more severe pathological manifestations. CONCLUSION: The gene chip test has a high specificity and sensitivity in detection of H.pylori infection, and is useful for finding the relationship between H.pylori virulence factors and the severity of disease.