Protocol biopsies are performed to detect subclinical pathologies that may lead to future graft dysfunction. However, they are not routinely performed interventions in every transplant center. There is no established regimen for performing them. The study aimed to evaluate if protocol biopsies can improve long-term patient outcomes after detecting early disorders and modifying treatment. Our observational study included 61 patients who underwent protocol biopsy 12 months after the transplantation. Based on the biopsy results, patients with abnormal histologic material (n=37) were divided into 3 study groups as follows: patients with mild inflammatory lesions (n=21), patients with interstitial fibrosis and tubular atrophy (IFTA) grade II to III (n=12), and patients with BK virus nephropathy (n=4). The control group (n=24) included kidney recipients with IFTA 0 to I grade. Outcomes after 5-year follow-up were evaluated. Five years after the biopsy, patients in the control group had stable graft function (5-year change in serum creatinine was -0.09 mg/dL). An increase in serum creatinine levels was observed in patients with IFTA II to III compared with the control group (0.14 mg/dL, P=.04). Immunosuppressive treatment was modified in the group with mild inflammatory changes and in the BKV group after the biopsy result. In the group with mild inflammatory lesions, renal function was stable (change of serum creatinine was -0.01 mg/dL, P=.51). In the BKV nephropathy group, there was a significant reduction in serum creatine levels (-0.48 mg/dL, P=.016). The analysis showed no diagnostic value for serum creatinine concentration (95% CI 0.49-0.78, P=.08). Protocol biopsies are useful for detecting early pathologies and preventing allograft failure. They greatly benefit patients with detectable pathology that can be treated or in whom therapy modification is possible.