Hematopoietic cell transplantation (HCT) is an important curative treatment for children with high-risk hematologic malignancies and solid tumors, and increasingly, non-malignant diseases. Given improvements in care, there is a growing number of long-term survivors of pediatric HCT. Compared with non-transplanted childhood cancer survivors, HCT survivors have been shown to have a substantially increased burden of serious chronic conditions and impairments involving virtually every organ system and overall quality of life. This likely reflects the joint contributions of pre-transplant treatment exposures and organ dysfunction, the transplant conditioning regimen, and any post-transplant graft versus host disease (GVHD). In response, the Children鈥檚 Oncology Group (COG) has created Long-Term Follow-Up Guidelines (www.survivorshipguidelines.org) for survivors of childhood, adolescent, and young adult cancer, including those treated with HCT. Guidelines taskforces, consisting of HCT specialists, other pediatric oncologists, radiation oncologists, organ-specific subspecialists, nurses, social workers, other healthcare professionals, and patient advocates have systematically reviewed the literature with regards to late effects after childhood cancer and HCT since 2002, with the most recent review completed in 2013. For the most recent review cycle, over 800 articles from the medical literature relevant to childhood cancer and HCT survivorship were reviewed, including 586 original research articles. Provided here-in is an organ system-based overview that emphasizes the most relevant COG recommendations (with accompanying evidence grade) for the long-term follow-up care of childhood HCT survivors (regardless of current age) based on a rigorous review of the available evidence. These recommendations cover both autologous and allogeneic HCT survivors, those transplanted for non-malignant diseases, and those with a history of chronic GVHD.