Objective　To investigate the incidence of Helicobacter pylori (H.pylori) infection in children with gastroduodenal diseases and to analyze the drug resistance of H.pylori isolates in Jiangxi. Methods　A total of 195 children with upper digestive tract symptoms were performed endoscopy and gastric biopsy from July 2014 to May 2015. H.pylori isolates were identified in incubated gastric mucosa. The H.pylori isolates resistant to amoxicillin, clarithromycin, and metronidazole were detected by E-test, and resistance to furazolidone were detected by K-B test. Results　A total of 80 H.pylori strains were isolated from gastric biopsy specimens in 195 children. The detection rate was 41.0%. Of all children, the detection rate in chronic superficial gastritis, duodenal bulb inflammation, gastric ulcer and duodenal bulb ulcer was 28.2%, 52.0%, 30.0% , and 51.2%, respectively. The resistance rate of H.pylori isolates to clarithromycin and metronidazole was 25.0% and 48.8%, respectively. The dual-resistance of H.pylori isolates to clarithromycin and metronidazole was 10%. No resistance of H.pylori isolates to amoxicillin and furazolidone was observed. Conclusions　H.pylori infection is a major cause of upper digestive tract disease in children. The resistance rate of H.pylori isolates to clarithromycin and metronidazole is high in Jiangxi.