We describe a well documented case of a fatal Phoma exigua lung infection in a patient with acute myeloid leukaemia and diabetes. The infection was histology and culture proven and a PCR assay was developed for detecting P. exigua DNA in deparaffinized lung-biopsy material. Confirmation of rare fungal pathogen infections requires a multidisciplinary approach involving clinical observations, mycology, histopathology and radiology.