We report a 6-year-old female with congenital bone marrow failure, who was referred for allogeneic stem cell transplantation. An initial work-up in infancy had not revealed any consistent symptoms associated with an inherited syndrome. Computed tomography of her abdomen for gastrointestinal bleeding after transplantation incidentally revealed a fat-replaced pancreas and led to the molecular diagnosis of Shwachman-Diamond syndrome (SDS) in the absence of clinical exocrine pancreatic insufficiency. We conclude that SDS may escape the clinical consensus criteria for the disease. Increased awareness of unusual presentations may allow confirming the suspected diagnosis by molecular analysis and ensure optimal management.