AR is considered as a risk factor for CAN after kidney TX. We combined data on AR with long-term graft function and histopathology to assess whether early treatment of AR is beneficial for long-term graft outcome in small children. Seventy-seven children with a mean age of 4.7 yr were studied. Early AR were diagnosed with FNAB and treated with methylprednisolone already before clinical signs occurred. The children were grouped into three groups (clinical, subclinical, and no AR) and then followed prospectively up to seven yr after TX with measured GFR and core needle biopsies to assess histopathological findings with the CADI score. Early AR, whether clinical or subclinical, did not affect long-term graft survival (80% with AR vs. 83% without AR, at 10 yr). Late AR, more than one yr after TX, had an inferior graft survival 50% vs. 84% (p = 0.02). GFR declined and the CADI scores increased with time, but there were no significant differences between the three groups. Prompt and early treatment of post-operative AR gives favorable long-term graft function compared with children without AR. Late AR is a risk factor for inferior long-term graft function.