Patients with neutropenia lasting for more than 10d, who develop fever and pulmonary infiltrates, are at risk of treatment failure under conventional broad-spectrum antibacterial therapy. Filamentous fungi are predominant causes of failure, however, multi-resistant gram-negative rods such as Pseudomonas aeruginosa or Stenotrophomonas maltophilia may be involved. Prompt addition of mould-active systemic antifungal therapy, facilitated by early thoracic computed tomography, improves clinical outcome. Non-culture-based diagnostic procedures to detect circulating antigens such as galactomannan or 1,3-beta-d-glucan, or PCR techniques to amplify circulating fungal DNA from blood, bronchoalveolar lavage or tissue specimens, may facilitate the diagnosis of invasive pulmonary aspergillosis. CT-guided bronchoalveolar lavage is useful in order to identify causative microorganisms such as multidrug-resistant bacteria, filamentous fungi or Pneumocystis jiroveci. For pre-emptive antifungal treatment, voriconazole or liposomal amphotericin B is preferred. In patients given broad-spectrum azoles for antifungal prophylaxis, non-azole antifungals or antifungal combinations might become first choice in this setting. Antifungal treatment should be continued for at least 14 d before non-response and treatment modification are considered. Microbial isolates from blood cultures, bronchoalveolar lavage or respiratory secretions must be critically interpreted with respect to their aetiological relevance for pulmonary infiltrates.