Non-endocrine events represent a heterogeneous group of complications occurring in children who survive long term after haematopoietic SCT. This review highlights the late sequel in a growing child. The preparative regimen itself with high-dose chemotherapy and/or radiotherapy (TBI) or the treatment given before the transplant procedure may cause organ damage with permanent sequel. Immune reconstitution and chronic GvHD have crucial role in occurrence of clinical abnormalities and late severe infections. Autoimmune syndromes may occur after use of novel transplant modalities (cord blood transplantation, reduced intensity conditioning regimen and haploidentical T-cell-depleted SCTs). Exposure to chemo- and/or radiotherapy increases the risk of second malignant neoplasms. Surveillance strategy focusing on each potential complication risk at continuous follow-up will allow vigilant post transplant care. Each paediatrician must be well versed in appropriate monitoring of these complications. Guidelines and recommendations are provided for serious problems occurring at follow-up, which must rapidly be identified so that appropriate intervention can be initiated. To achieve cure at a lowest possible price in terms of suffering and cost expenditures for health care is an extended frontier of paediatric haematopoietic SCT and biggest challenge for a paediatrician.