Invasive aspergillosis affects 3 to 11% of BMT patients with a high mortality rate (60 to 95%). Extra-pulmonary disease is an unusual event, and primary renal aspergillosis is extremely uncommon. A patient with CML treated with BMT, who developed primary renal and subsequently hepatic aspergillosis, is described. Dysfunction of the mucosal barrier secondary to conditioning therapy, was a possible portal of entry for the fungus. Fine needle aspiration was very useful, as is direct microscopic examination of the urine, for diagnosis of the fungal infection. Surgical drainage of the abscess followed by antifungal therapy is the treatment of choice. Unconducive situations, such as refractory thrombocytopenia, are associated with the worst outcome in these patients.