The clinical significance of C4d positivity in patients with stable graft function is undetermined. This study evaluated the clinical outcome of protocol biopsy-proven C4d-positive renal transplants with stable graft function in the early post-transplantation period. Protocol biopsies (n = 79) were performed on stable allografts on the 14th post-transplant day, and indication biopsies (n = 74) were performed on dysfunctioning allografts within one yr after transplantation. Clinical and histological findings, graft function and graft survival rates were compared between C4d-positive and C4d-negative grafts in each group. The incidence of C4d positivity was 5.1% in protocol biopsies and 9.5% in indication biopsies. In protocol biopsies, C4d-positive allografts showed minimal tubulointerstitial inflammation, and the graft function and graft survival rate did not differ from C4d-negative allografts. All C4d-positive allografts maintained stable graft function without anti-rejection therapy, and follow-up biopsies of two patients showed no C4d deposition or evidence of rejection. On the other hand, C4d-positive allografts in indication biopsies showed severe tissue injury, and the graft survival rate was significantly lower than C4d-negative allografts. In conclusion, C4d-positive allografts with stable graft function in the early post-transplantation period take an indolent course.