Pulmonary mycoses count among the most dangerous complications in allogeneic hematopoietic stem cell transplantation. Despite the establishment of antifungal chemoprophylaxis and empirical antifungal treatment, they frequently lead to respiratory failure and are still associated with an extraordinarily poor prognosis. However, the emergence of new antimycotics with alternative mechanisms of actions and decreased toxicity in combination with the development of new non culture-based diagnostic techniques may allow earlier, more aggressive and more effective antifungal treatment approaches. In addition, the optimized use of new technologies designed to augment spontaneous breathing efforts by patients, mechanical ventilation, as well as the advantages of early tracheostomy lead us to expect better outcomes in the treatment of respiratory failure due to pulmonary mycoses following allogeneic hematopoietic stem cell transplantation.