Pulmonary infiltrates in immunocompromised children often pose problems in terms of deciding on further diagnostic and therapeutic procedures, but few studies have evaluated the value of non-invasive and invasive diagnostic methods in paediatric populations. Both galactomannan ELISA and PCR protocols appear to be less useful in children than in adults. Invasive procedures, such as bronchoalveolar lavage or lung biopsy, can yield a pathohistological diagnosis and/or the isolation of a pathogen. Prospective studies in paediatric patients are needed urgently to assess the value of different diagnostic procedures and to define an effective and safe diagnostic strategy for the individual child.