Allogeneic hematopoietic stem cell recipients require specific long term follow-up. They are thus susceptible to develop late complications, either haematological or non haematological. The first year is characterized by the risk of chronic graft versus host disease and infections. Metabolic- and organ toxicity as well as potential secondary malignancy require very long-term follow-up. Prevention and early treatment by a multidisciplinary team are essential for the optimal management of these patients.