Shwachman-Diamond syndrome (SDS) is a rare autosomal recessive disease characterized by exocrine pancreatic insufficiency with malabsorption, malnutrition, growth failure and bone marrow failure. Furthermore, duodenal inflammatory enteropathy features may be present. For the first time, we report here a SDS case that is also diagnosed with inflammatory bowel disease (IBD). He was diagnosed with SDS at the age of two based on poor growth, severe exocrine pancreatic insufficiency with steatorrhea, neutropenia, recurrent infections and thoracic skeletal abnormalities. Ileocolonoscopy and histopathology revealed colonic Crohn's disease at the age of sixteen. Our report may encourage further studies elucidating the possible association between the SDS genetic defect and inflammatory bowel disease.