To evaluate which factors influence eradication success with standard triple therapy for Helicobacter pylori. A prospective study was made of 891 patients infected by H. pylori and diagnosed with duodenal ulcer (n=422), gastric ulcer (n=221), or functional dyspepsia (n=248). Initially, an endoscopy with biopsies of antrum and body (haematoxylin-eosin stain), and a 13C-urea breath test were performed. All patients were treated for seven days with either omeprazole 20 mg twice daily in 442 patients (OCA) or pantoprazole 40 mg twice daily in 449 patients (PCA), associated to clarithromycin (500 mg twice a day) and amoxicillin (1 g twice a day). Two months after completing therapy urea breath test was repeated to confirm eradication. Mean age +/- SD was 51.6 +/- 15 years, 61% were male. Overall eradication rate was 73.7% (95% CI 69-77%) and 80.8% (77-84%) with OCA and PCA therapy, respectively, showing significant difference between treatment regimens (chi 2 =6.3; p= 0.01). As refers to underlying diseases, H. pylori eradication was achieved in 77.4% (74-80%) of peptic ulcers and 77% (71-82%) of functional dyspepsia (p=n.s.). With our two treatment regimens (OCA/PCA) eradication success was 74/81% in peptic ulcer (p=0.03), and 72/80% in functional dyspepsia (p=0.1). In the multivariate analysis, type of therapy was the only variable that correlated with eradication success (odds ratio 1.5; 95% CI: 1.1-2.1) (chi2 model: 6,4; p=0.01). Standard triple therapy containing a proton pump inhibitor, clarithromycin and amoxicillin for seven days achieves in our community a moderate eradication success; this result could improve by using pantoprazole instead of omeprazole. This therapy is equally effective in patients with peptic ulcer and functional dyspepsia.