Hematopoietic stem cell transplant (SCT) remains a curative option for a variety of malignant and non-malignant disorders in children. Following transplant a proportion of SCT recipients become critically ill and need intensive care. Critical illness may occur in the setting of transplant complications such as graft versus host disease (GVHD), idiopathic pneumonia syndrome (IPS), veno-occlusive disease (VOD) and transplant associated thrombotic microangiopathy (TA-TMA). Hence, familiarity with recent advances in the transplant process and complications is crucial for the intensivist. This article will highlight common complications encountered in the critically ill SCT recipient.