Up to 60% of patients with haematological malignancy will develop pulmonary infiltrates at some point in their disease course. Bronchoscopy should be used early in patients without respiratory failure as diagnostic yield is highest in the first 1–2 days of illness. Perceptions that patients with haematological malignancy are at higher risk of complications from bronchoscopy has led to a reluctance to perform the procedure. However, cohort studies have not demonstrated any increase in complications for this specific patient group. Common concerns include mucosal injury, respiratory impairment and haemorrhage. However, prospective cohort studies demonstrate that this patient group do not experience a higher than baseline level of complications. Specific pathogen diagnosis reduces morbidity and mortality in lung infection. Additionally, complex infections with multidrug-resistant organisms, the increasing prevalence of which is largely driven by empirical antibiotic use, make specific diagnosis more crucial than ever if we are to maintain our ability to manage myelosuppressive therapies and stem cell transplant.