In a prospective study, thirty consecutive patients presenting with either H.pylori positive (histology and/or culture) ulcer disease (n = 17; acute ulcer: n = 11) or functional dyspepsia (n = 13) were treated over one week with pantoprazole 40 mg bd, clarithromycin 250 mg bd and metronidazole 400 mg bd. Four weeks after discontinuation of the study medication H.pylori eradication was assessed by means of an urease test, culture and histology. One patient had to be withdrawn from the study after one day because of a concomitant infectious disease requiring long-term antibiotic treatment. Another patient refused the final follow-up endoscopy. 28 patients completed the study without contravening the protocol. H.pylori infection was eradicated in 24 out of 28 patients (eradication rate: 86%; 95%-confidence interval: 57%-96%). Cure of bacterial infection was more frequently obtained in ulcer patients as compared to patients suffering from functional dyspepsia (94% vs 75%; p = 0.28). In 2 patients, treatment failure was associated with pretherapeutic resistance of H. pylori to either clarithromycin or metronidazole. Without antiulcer treatment beyond eradication therapy, ulcer healing was endoscopically confirmed after 5 weeks in 9 out of 10 patients available for follow-up (healing rate: 90%; 95%-confidence interval: 56%-100%). Seven patients reported mild adverse events that did not lead to discontinuation of the study medication (rate: 23%; 95%-confidence interval: 10%-42%). After cure of the infection, histology demonstrated a statistically highly significant improvement (p < 0.001) of both grade and activity of antrum and body gastritis.(ABSTRACT TRUNCATED AT 250 WORDS)