We performed quantitative PCR-based serial chimerism testing of whole blood (WB) and CD3 þ cells and retrospectively correlated the results of chimerism tests and the risk of graft loss in children undergoing transplant for non-malignant disorders. Twenty-four children were included in this study. All patients initially engrafted; subsequently, 12% lost the graft, 21% achieved complete donor chimerism and 67% had mixed chimerism (MC). Patients underwent delayed taper of cyclosporine (CsA) if they had MC. Overall survival was 87 ± 7% (s.d.) at 5-years post transplant, and it was not affected by chimerism status. Both WB and CD3 þ chimerism showed significant fluctuations with a peak in autologous cell signal occurring at a median of 7 months for WB and 2 months for CD3 þ cells. Initial post transplant chimerism percentage in either WB or CD3 þ lineage was not related to graft loss. Increasing MC to 430% host cells was seen in 33% of patients, and it was related to increased risk of graft loss, as previously published. However, 63% of children with increasing MC did not lose their graft. Additional studies of post transplant chimerism are required to improve our ability to accurately identify children at risk of graft loss following transplant for non-malignant disorders.