A 50-year-old man presented with bloody diarrhea and 25-kg weight loss over 3 months. Upper and lower endoscopy showed diffuse shaggy white villi in the duodenum and terminal ileum. In addition, capsule endoscopy and double-balloon enteroscopy revealed shaggy white villi in the entire small intestine. Histological examination of biopsy specimens found the lamina propria of the duodenal and intestinal mucosa to be densely infiltrated by rich foamy macrophages that were periodic acid-Schiff-positive. Electron microscopy showed numerous bacilli in the lamina propria. Tropheryma whipplei DNA was detected in the specimens by polymerase chain reaction. Based on these findings, the patient was diagnosed with Whipple's disease. He was treated with a 2-week course of ceftriaxone followed by trimethoprim-sulfamethoxazole. At the 2-month follow up, diffuse white shaggy villi improved dramatically.