Although hematopoietic stem cell transplantation (HSCT) can be curative in patients with certain malignancies, survival is poor if the recipient becomes critically ill. This prospective study examined the outcomes of 115 consecutive HSCT patients admitted to the medical intensive care unit (MICU) of a tertiary cancer center and identified variables associated with survival. The need for endotracheal intubation and mechanical ventilation ("intubation") had a profound adverse effect on survival. Overall, 9 of 48 (18.8%) intubated patients survived compared with a survival rate of 44 of 67 (65.7%) among patients not intubated (p < 0.001). This pattern persisted for nearly all patient subgroups. Among intubated patients, those receiving peripheral blood stem cell transplant (PBSCT) had significantly better survival than bone marrow transplant (BMT) patients (8 of 26, 31% versus 1 of 22, 4%; p = 0.028). Multiple logistic regression analyses indicated that the probability a patient admitted to the MICU survived decreased significantly if the patient was intubated, had an allogeneic rather than autologous transplant, had an infection or gastrointestinal bleeding, and also decreased with higher respiratory rate, higher heart rate, longer time from transplant to MICU admission or higher bilirubin. These results may be of value in deciding which critically ill patients will benefit from intubation following major complications after HSCT transplantation.