Objectives: To determine the quality of duodenal ulcer healing following treatment with standard regimens of Helicobacter pylori eradication, or with omeprazole, ranitidine and de nol. Design: The study was designed to determine whether changes in gastric metaplasia and microvilli occur at an ultrastructural level before and after various treatments. Patients and methods: Twelve patients with duodenal ulcers (nine males, three females), all judged positive for H. pylori by the [C-13]-urea breath test, were studied. Biopsies were obtained immediately before treatment and 1 month later. Four standard treatment regimens were instituted for 1 month, comprising (1) 1 week of eradication therapy (one tablet de nol each day, 500 mg amoxycillin each day and 2 g metronidazole on each of the last 3 days), (2) 40 mg omeprazole each morning, (3) 300 mg ranitidine each morning and (4) one tablet de nol each day. The groups were matched for age and sex. Gastric (fundus, body and antrum) and duodenal biopsies (edge of duodenal ulcer or its scar) were taken and studied by light microscopy; the duodenal biopsies were also examined by electron microscopy. All ulcers were endoscopically healed after 1 month. Results: After treatment, all the biopsies in the eradication group were negative for H. pylori, but present in one or more sites in all the other treatment groups. However, the duodenal inflammatory response decreased in all groups. There was no apparent change in gastric metaplasia or the quality of microvilli in response to any of the four treatments. Conclusions: Healing of ulcer sites after eradication of H. pylori is a prolonged process. At the ultrastructural level, epithelial integrity was not restored within the time-scale of this study.