Presence of subclinical rejection (SCR) with IF/TA in protocol biopsies of renal allografts has been shown to be an independent predictor factor of graft loss. Also, intragraft Foxp3+ Treg cells in patients with SCR has been suggested to differentiate harmful from potentially protective infiltrates. Nonetheless, whether presence of Foxp3 Treg cells in patients with SCR and IF/TA may potentially protect from a deleterious graft outcome has not yet been evaluated. This is a case-control study in which 37 patients with the diagnosis of SCR and 68 control patients with no cellular infiltrates at 6-month protocol biopsies matched for age and time of transplantation were evaluated. We first confirmed that numbers of intragraft Foxp3-expressing T cells in patients with SCR positively correlates with Foxp3 demethylation at the Treg-specific demethylation region. Patients with SCR without Foxp3+ Treg cells within graft infiltrates showed significantly worse 5-year graft function evolution than patients with SCR and Foxp3+ Treg cells and those without SCR. When presence of SCR and IF/TA were assessed together, presence of Foxp3+ Treg could discriminate a subgroup of patients showing the same graft outcome as patients with a normal biopsy. Thus, presence of Foxp3+ Treg cells in patients with SCR even with IF/TA is associated with a favorable long-term allograft outcome.