Peptic ulcer disease (PUD) occurs after a long-term Helicobacter pylori infection. However, the disease can develop earlier, and rare cases have been observed in children, suggesting that these H. pylori strains may be more virulent. We used suppressive subtractive hybridization for comparative genomics between H. pylori strains isolated from a 5-year-old child with duodenal ulcer and from a sex-and age-matched child with gastritis only. The prevalence of the 30 tester-specific subtracted sequences was determined on a collection of H. pylori strains from children (15 ulcers and 30 gastritis) and from adults (46 ulcers and 44 gastritis). Two of these sequences, jhp0562 (80.0% versus 33.3%, P ؍ 0.008) and jhp0870 (80.0% versus 36.7%, P ؍ 0.015), were highly associated with PUD in children and a third sequence, jhp0828, was less associated (40.0% versus 10.0%, P ؍ 0.048). Among adult strains, none of the 30 sequences was associated with PUD. However, both jhp0562 and jhp0870 were less prevalent in adenocarcinoma strains than in PUD strains from children and adults, the difference being statistically significant for jhp0870. In conclusion, two H. pylori genes were identified as being strongly associated with PUD in children, and their putative roles as an outer membrane protein for jhp0870 and in lipopolysaccharide biosynthesis for jhp0562, suggest that they may be novel virulence factors of H. pylori.Helicobacter pylori, a spiral-shaped gram-negative bacterium, can lead to various gastroduodenal diseases. A causal association has been established with chronic gastritis, peptic ulcer, gastric adenocarcinoma, and gastric mucosa-associated lymphoid tissue (MALT) lymphoma (10). The mechanisms for such a clinically diverse profile are not totally clear but may include host and environmental factors, as well as bacterial virulence factors (7,20,23,47).In adult patients, severe gastroduodenal diseases such as duodenal ulcer, gastric adenocarcinoma, and MALT lymphoma occur after a long-term colonization (22, 47), while the onset of H. pylori infection is essentially during childhood (26). Indeed, the majority of H. pylori-infected children remain asymptomatic, except for a very small group which will develop peptic ulcer. Other factors such as nonsteroidal anti-inflammatory drug use, physiologic stress, and vascular insufficiency also play an important role beside H. pylori infection in the development of peptic ulcer in children (28). Moreover, colonization with H. pylori strains that are considered virulent in adults does not always correlate with the severity of endoscopic and histologic findings in children (24). These conflicting results may be due to the short-term infection, the association becoming possibly stronger as the duration of infection increases (53). Ulcers in children, in contrast to adults, appear shortly after H. pylori colonization, suggesting that differences exist between the ulcerogenic strains which infect children and adults and that strains associated with peptic ulcer in children may be m...