We examined whether a single inoculation of Helicobacter pylori can colonize the stomachs of ulcerated rats and delay their healing and whether an antibiotic drug and acid pump inhibitors can enhance the ulcer healing in infected rats. Ulcers were produced by a submucosal injection of acetic acid solution into the gastric wall. Helicobacter pylori (ATCC-43504) was inoculated into rats with and without gastric ulcers. The animals were killed 2, 4, 6, 8 or 10 weeks after the inoculation and the ulcerated area and H. pylori viability were determined. Each test drug and their combination was administered for 1 or 2 weeks after H. pylori inoculation. Helicobacter pylori could not colonize the stomachs of normal rats, but could colonize stomachs with ulcers for 10 weeks at an incidence of > 80%. Spontaneous healing of gastric ulcers was delayed by H. pylori infection during these 10 weeks. Daily treatment with clarithromycin significantly and dose-dependently delayed ulcer healing in infected rats. Both omeprazole and leminoprazole significantly enhanced ulcer healing and inhibited the clarithromycin-delayed ulcer healing. We conclude that: (i) H. pylori can colonize rat stomachs with ulcers and delay ulcer healing; (ii) clarithromycin delays ulcer healing in H. pylori-infected rats; and (iii) acid pump inhibitors inhibited the clarithromycin-delayed ulcer healing.