Patients with duodenal ulcer or functional dyspepsia do not differ on dyspeptic symptoms. The aim of the present study was to test the hypothesis that functional dyspepsia and duodenal ulcer are two different diagnostic entities by examining the discriminating power of several anamnestic, biological, and psychosocial variables. Ninety-four patients with duodenal ulcer and 86 patients with functional dyspepsia were included. Anamnestic data, global assessment, Helicobacter pylori status, blood group, Lewisa+ phenotype, and several measures of psychological distress and somatic complaints were registered. Compared to patients with functional dyspepsia, the duodenal ulcer patients were more often infected by Helicobacter pylori and had their stomach discomfort more often relieved by eating. Compared to patients with duodenal ulcer, patients with functional dyspepsia had higher scores of depression, trait anxiety, general psychopathology and different somatic complaints (called somatization). They were also less satisfied with the health care system, their disorder had a greater negative impact on their quality of life, and their global assessment of own health was poorer. Discriminant analysis including age, smoking, Helicobacter pylori status, global assessment, and somatic complaint classified 86.1% of the patients correctly (77.9% of the patients with functional dyspepsia and 93.6% of the patients with duodenal ulcer). It is concluded that duodenal ulcer and functional dyspepsia are two separate diagnostic entities. Patients with duodenal ulcer are older, smoke more often, and almost all are infected with Helicobacter pylori, while patients with functional dyspepsia are characterized by somatization and a negative assessment of their own health.