Background: Magnification endoscopy and chromoendoscopy together have been used to evaluate mucosal detail in a number of conditions, including Barrett's esophagus and flat colonic polyps, but they have not been used to evaluate villous atrophy in the proximal small intestine. Methods: Thirty-four patients suspected of having a malabsorption syndrome (either celiac disease or tropical sprue) were evaluated using an Olympus magnification gastroscope in both normal and high magnification settings. Indigo carmine dye spraying techniques were used to assist in evaluating duodenal mucosa for evidence of villous atrophy. The accuracy of endoscopically predicted villous atrophy was assessed by histologic evaluation of biopsy specimens taken in the descending duodenum. Results: Magnification endoscopy with dye spraying was both highly sensitive (94%) and specific (88%) in identifying patients with villous atrophy. This technique was more accurate (91%) in identifying patients with partial atrophy than standard endoscopy (9%, p < 0.01) and was also useful in identifying patients with patchy villous atrophy (5 of 5) to allow directed biopsies of abnormal tissue. Conclusion: Magnification endoscopy with chromoendoscopy is a promising technique for the evaluation of patients with suspected malabsorption. This technique is especially valuable in patients with partial atrophy, where villous abnormalities can be patchy and the duodenum usually appears normal during standard endoscopy. (Gastrointest Endosc 1997;46:226-30.)