Allogeneic hematopoietic stem cell transplantation (HSCT) is a curative treatment option for various hematologic disorders. However, life-threatening adverse events resulting from treatment-related toxicity, severe infections, and/or graft-versus-host disease (GvHD) can occur. We report on a 64-year-old patient suffering from secondary acute myeloid leukemia (AML) who underwent successful allogeneic HSCT while on invasive mandatory ventilation (IMV). The patient received reduced intensity conditioning (RIC) according to the FLAMSA-protocol. Acute respiratory failure occurred one day before scheduled HSCT. Following emergency endotracheal intubation the patient was transferred to the intensive care unit (ICU). Because of respiratory deterioration, stem cell infusion was postponed. After stabilization of respiratory parameters, HSCT was performed during IMV which was continued for seven days. Following hematopoietic regeneration the patient was discharged in good condition on day 35 after HSCT. This case illustrates that intubation and mechanical ventilation do not necessarily exclude leukemic patients from HSCT.