Few virulence determinants of Helicobacter pylori have been tested in vivo. We conducted this study to establish an animal model for their screening. Six-week-old male Mongolian gerbils were inoculated with wild-type H. pylori (TN2) or its isogenic mutant with deletion of cagE (TN2DeltacagE), total cag pathogenicity island (TN2DeltacagPAI), HP0499 (TN2DeltaHP499), or HP0638 (TN2DeltaHP638) (n=5 each). The animals were killed 3 weeks later, and the density of bacteria and the degree of inflammation in the stomach were compared. Infection was established in all animals except those inoculated with TN2DeltaHP638. TN2 and TN2DeltaHP499, but not TN2DeltacagE and TN2Deltacag PAI, induced intense inflammation, although the densities of bacteria were similar. The Mongolian gerbil model was useful for the screening of virulence determinants in vivo, which confirmed the importance of cag PAI while questioning that of HP0499.