Historically, the mortality of patients admitted to the ICU after allogeneic stem cell transplantation (alloSCT) is high. Advancements in transplantation procedures, infectious monitoring and supportive care may have improved the outcome. This study aimed to determine short-term and long-term mortality after ICU admission of patients after alloSCT and to identify prognostic clinical and transplantation-related determinants present at ICU admission for long-term outcome. A multicenter cohort study was performed to determine 30-day and 1-year mortality within 2 years following alloSCT. A total of 251 patients were included. The 30-day and 1-year mortality was 55% and 80%, respectively. Platelet count <25 × 109/L (OR: 2.26, CI: 1.02–5.01) and serum bilirubin >19 μmol/L (OR: 2.47 CI: 1.08–5.65) at admission, other donor than a HLA-matched-related or HLA-matched-unrelated donor (OR: 4.59, CI: 1.49–14.1) and vasoactive medication within 24 h (OR: 2.35, CI: 1.28–4.31) were associated with increased 30-day mortality. Other donor than a HLA-matched-related or HLA-matched-unrelated donor (OR: 1.9, CI: 1.13–3.19), serum bilirubin >77 (OR: 2.05, CI: 1.28–3.30) and vasoactive medication within 24 h (OR: 1.65, CI: 1.12–2.43) were associated with increased 1-year mortality. Neutropenia was associated with decreased 30-day and 1-year mortality (OR: 0.29, CI: 0.14–0.59 and OR: 0.70, CI: 0.48–0.98). Myeloablative conditioning and T cell-depleted transplantation were not associated with increased mortality.