Neurological complications are a relevant cause of morbidity and mortality after haematopoietic stem cell transplantation (SCT). We retrospectively analysed neurological complications of 165 paediatric patients who underwent SCT between 1996 and 2003. In all, 111 (67%) transplantations were allogeneic and 54 (33%) transplantations were autologous. Post-SCT neurological complications were seen in 24% of patients. They were seen in six children after autologous SCT and in 11 and 23 cases after allogeneic-related and -unrelated SCT. Neurological symptoms occurred between day +22 and +912 after transplantation and were classified into two groups. The first group (n=21) offered non-repetitive symptoms lasting less than 24 h without any cerebral imaging and cerebrospinal fluid(CSF) abnormalities. The second group (n=19) was characterized by progressive neurological symptoms, pathological MRI findings and/or abnormal results in CSF. Those with a progressive clinical course resulted from infections (n=10), drug toxicity (n=5), cerebrovascular events (n=2) and the central nervous system (CNS) relapse of the underlying disease (n=2). In particular, cerebral aspergillosis and toxoplasmosis after allogeneic unrelated SCT are a major challenge and are associated with a high mortality. In conclusion, our data suggest that patients presenting with progressive neurological symptoms after SCT require prompt diagnostic procedures and initiation in antimicrobial therapy in case of any findings suggestive of CNS infection.