Hematopoietic stem cell transplantation (HSCT) can cause various complications involving lung, liver, intestine and other organs. Chemotherapy, radiation therapy, and graft-versus-host disease (GVHD) may injure the cells in the intestinal mucosa of HSCT recipients. Pneumatosis cystoides intestinalis (PI) is a condition that presence of air in the bowel wall is demonstrated by radiologic or pathologic tests. It is one of the infrequent complications after HSCT and is associated with several medical and surgical conditions. However its pathogenesis and definite etiologic factors are still unknown. Here, we present a case of PI in a HSCT recipient, who was diagnosed of bronchiolitis obliterance accompanied with chronic GVHD and pulmonary disease caused by Mycobacterium abscessus.