Background: To understand if relapse, following antimicrobial treatment was due to re-infection or to recrudescence. Methods: Fifty patients with dyspepsia were studied prospectively. They were followed up by endoscopy and biopsy of antral mucosa before and after treatment with anti-microbial therapy. Gel isoelectrofocusing was used to characterize protein profile of Hp. Results: At baseline 40 patients were affected by chronic gastritis associated with Hp. At the end of treatment 75% patients given omeprazole, amoxicillin and clarithromycin were Hp infected: 43% showed the same protein profile and 57% different. Conclusions: Our data suggest that the relapse is due to recrudescence or to reinfection