Crohn's disease (CD) not uncommonly affects the stomach and duodenum, but its histologic appearance is not well described beyond the identification of granulomas. We retrospectively identified 209 upper gastrointestinal biopsy samples from 80 sets of biopsies from 49 patients with CD. Age- and sex-matched control biopsies were selected from recent cases of Helicobacter pylori gastritis (73 biopsy samples from 34 patients), from patients with a known history of nonsteroidal antiinflammatory drug use (18 biopsy samples from 12 patients), and from three patients with ulcerative colitis. Architectural and inflammatory changes were evaluated and compared. Over three fourths of the patients with CD had abnormal biopsy results. Fifty-six percent of patients with CD had acute inflammation, but only 10% of the patients were infected with H pylori. Focal acute inflammation was a characteristic of H pylori-negative CD (stomach, 31%; duodenum, 40%), which was much less common in the non-CD group (stomach, 2%; duodenum, 8%). Surface intraepithelial neutrophils of the duodenum were more common in H pylori-negative patients with CD (25%) than in those who did not have CD (4%), and deep acute inflammation of the duodenum was more likely in H pylori-negative patients with CD (19% vs. 0%). Granulomas were found in only 9% of the CD group. Focal acute inflammation of the gastroduodenum, especially in a background of noninflamed mucosa, is strong evidence for CD in the appropriate clinical context, but the stomach and duodenum must be properly sampled and carefully examined for any evidence of H pylori.