Survival of allogeneic hematopoietic stem cell transplant (aHSCT) recipients in the intensive care unit (ICU) has been poor. We retrospectively analyzed the short- and long-term outcomes of aHSCT patients admitted to the ICU over a 12-year period. Of 1235 adult patients who had aHSCT between 2002 and 2013, 161 (13%) were admitted to the ICU. The impact of clinical parameters was assessed and outcomes were compared for the periods 2002–2007 and 2008–2013. The ICU, in-hospital, 1- and 5-year survival rates were 64.6 %, 46%, 33% and 20%, respectively. Mechanical ventilation and vasopressor use predicted for worse hospital- and overall survival. After 2008, the requirement for mechanical ventilation and vasopressors, and the diagnosis of sepsis were reduced. While hospital mortality decreased from 69% to 44%, long-term survival remained unchanged. Late deaths, due to causes not associated with the ICU such as relapse and graft-versus-host disease, increased. As thresholds for transplant are lowered, improvements in ICU outcomes for aHSCT recipients may be limited.