Evidence-based guidelines for the treatment of established fungal infections in the adult haematology/oncology setting were developed by a national consensus working group representing clinicians, pharmacists and microbiologists. These updated guidelines replace the previous guidelines published in the Internal Medicine Journal by Slavin et al. in 2004. The guidelines are pathogen-specific and cover the treatment of the most common fungal infections including candidiasis, aspergillosis, cryptococcosis, zygomycosis, fusariosis, scedosporiosis, and dermatophytosis. Recommendations are provided for management of refractory disease or salvage therapies, and special sites of infections such as the cerebral nervous system and the eye. Because of the widespread use newer broad-spectrum triazoles in prophylaxis and empiric therapy, these guidelines should be implemented in concert with the updated prophylaxis and empiric therapy guidelines published by this group. This section of the guidelines is dedicated to the management of established invasive antifungal infections (IFI) in the adult haematology/oncology setting. Our recommendations are based on the antifungal agents licensed for use in Australia at the time of writing, and are organized according to pathogen.Where there is a radiological abnormality on computed tomography (CT)/high resolution computed tomography (HRCT) without early microbiological confirmation, clinicians should consider the most common clinical scenario. Microbiological confirmation with histology and/or culture should be pursued in all cases where the patient's clinical status permits additional investigations, such as bronchoscopy and/or biopsy. Newer diagnostic modalities such as polymerase chain reaction (PCR), galactomannan (GM) testing and molecular sequencing, are becoming increasingly available, particularly at specialist centres, and will play an increasing role in identifying probable and proven fungal infections. They are discussed in detail in the previous section of the guidelines by Morrissey et al.When considering the possibility of mould infections, Aspergillus is still the most likely organism within the Australasian setting.