Abstract Background It is important to know the causes of dyspepsia to establish the therapeutic approach. Dyspepsia is a frequent syndrome in our country, where there are restrictions to endoscopy and high prevalence of Helicobacter pylori (H. pylori) infection. This study aimed to assess the endoscopic findings of the syndrome, in an outpatient screening clinic of a tertiary hospital in São Paulo. Methods Outpatients with uninvestigated dyspepsia, according to Rome III criteria, answered a dyspepsia questionnaire and underwent esophagogastroduodenoscopy. The Rapid Urease Test was applied to fragments of the antral mucosa and epidemiological data were collected from the studied population. Organic dyspepsia findings were analyzed with different variables to verify statistically significant associations. Results Three hundred and six patients were included and 282 were analyzed in the study. The mean age was 44 years and women comprised 65% of the sample. Forty-five percent of the patients reported alarm symptoms. Functional dyspepsia was found in 66% of the patients (20% with normal endoscopy results and 46% with gastritis), 18% had GERD and 13% had ulcers (duodenal in 9% and gastric in 4%). Four cases of gastric adenocarcinoma were identified (1.4%), one without alarm characteristics, 1 case of adenocarcinoma of the distal esophagus and 1 case of gastric lymphoma. The prevalence of H. pylori was 54% and infection, age and smoking status were associated with organic dyspepsia. The age of 48 years was indicative of alarm signs. Conclusions The endoscopic diagnosis of uninvestigated dyspepsia in our setting showed a predominance of functional disease, whereas cancer was an uncommon finding, despite the high prevalence of H. pylori . Organic dyspepsia was associated with infection, age and smoking status.