Pneumatosis cystoides intestinalis (PCI) is still a poorly understood phenomenon, currently considered to result from primary mucosal insult from varying causes. We report a case of severe PCI in a patient with chronic GVHD after bone marrow transplantation (BMT) performed to treat secondary AML. Post BMT, the patient suffered acute intestinal and cutaneous GVHD, eventually developing intestinal and biopsy-proven cutaneous chronic GVHD, which necessitated continuous steroid therapy. Chronic pancreatitis associated with GVHD was diagnosed by explorative surgery in February 2000 on the basis of increasing epigastric discomfort, tumour marker (CA 125) increase and the CT finding of a suspicious mass in the pancreas. Readmission occurred in April 2000 for rapid onset of inferior abdominal pain with distinct peritoneal signs. Relaparotomy, deemed necessary on the grounds of both clinical and radiological findings, revealed marked PCI of the ascending and transverse colon and attached mesentery in an otherwise intact gastrointestinal tract. Post-operative reconvalescence was uneventful, with no clinical or radiological recurrence of PCI in the following 10 months. In the context of a review of the relevant literature, this case report illustrates the complex underlying pathophysiology, and difficulty in making a differential diagnosis and treating PCI.