A 33-year-old man with myelodysplastic/myeloproliferative disease underwent allogeneic bone marrow transplantation. Around day 80 post-transplant, he complained of abdominal pain and diarrhea. Colonoscopy and esophagogastroduodenoscopy findings were unremarkable. Double-balloon enteroscopy revealed atrophic villi and mild erosions localized in the small intestine. Histological examination revealed marked proliferation of histiocytes with numerous acid-fast bacilli in their cytoplasm. The specific polymerase chain reaction for Mycobacterium tuberculosis was negative, and a diagnosis of intestinal non-tuberculous mycobacteria (NTM) was made. Physicians should recognize that NTM infection is one of the gastrointestinal infectious complications in immunocompromised patients such as bone marrow transplant recipients, and could localize in the small intestine.