We herein present the case of a 30-year-old man who developed recurrent pancreatitis and chronic graft-versus-host disease following unrelated bone marrow transplantation for acute myeloid leukemia (AML) with t(16;21)(p11;q22). Autoimmune pancreatitis was initially suspected due to the radiological findings and lack of response to gabexate mesilate and antibiotics. An examination of specimens successfully obtained via endoscopic ultrasound-guided fine needle aspiration (EUS-FNA) demonstrated invasion of AML cells in the pancreatic tissue. EUS-FNA is a less invasive method and a particularly useful diagnostic tool in severely ill patients.