Idiopathic hyperammonemia (IHA) has been described as a rare complication of intensive chemotherapy, but there is little data regarding its occurrence after bone marrow transplantation (BMT). IHA is defined as elevated plasma ammonia concentrations (> 200 mumol/l) in the absence of significant liver function abnormality. From a 21 year BMT database of 2358 patients, we have identified 12 patients (0.5%) with IHA, ages 19 to 46 years. Diagnoses included ALL (n = 2), AML (n = 4), CLL (n = 1), CML (n = 3) and aplastic anemia (n = 2). Eight received marrow from a matched sibling donor, three from an unrelated donor and one autologous marrow. IHA occurred between 14 and 106 days after transplant (median, 25 days). Most frequently patients presented with symptoms of a metabolic encephalopathy, with lethargy and confusion evolving into unresponsiveness, metabolic coma and in eight cases, seizures. At diagnosis of IHA, liver functions were normal or only modestly abnormal. Ten of the 12 patients died 1 to 9 days (median 3.5 days) after diagnosis of IHA despite treatment with combinations of dialysis and ammonia-trapping therapy. While IHA is a rare complication of BMT, it is associated with a high mortality. Early recognition of the syndrome by measurement of plasma ammonia concentrations in patients with neurological symptoms may improve outcome.