We presented a 20-year-old patient with Crohn′s disease (CD). Colonoscopy revealed longitudinal ulceration in the terminal ileum and rectal aphtoid ulcers. After treatment with mesalamine and total parenteral nutrition, repeat colonoscopy revealed a granular elevated area in the terminal ileum, which appeared as an irregular dome-like elevation with irregularly arranged villi on magnifying endoscopy. Biopsy specimens taken from the region showed microgranulomas and lymphoid hyperplasia. Scanning electron microscopy revealed the presence of M cells, confirming that the area corresponded to Peyer′s patches. Peyer′s patches by magnifying endoscopy and electron microscopy may provide insights into the pathogenesis of CD.