The role and timing of protocol biopsies after kidney transplantation are controversial. We changed our protocol biopsy policy and compared the predictive value of biopsies at different time-points. Protocol biopsies at 6 months (n = 45) were obtained during 2001-2004, and at 3 and 12 months from 2004 (n = 41). Donor biopsy was available from 70 patients. Histopathologic changes were described with chronic allograft damage index (CADI) and Banff 1997. Follow-up was for 18 months. Chronic allograft nephropathy (CAN) was present in 12%, 51%, and 34% and borderline or subclinical rejection in 9.8%, 8.9%, and 7.3% of patients at 3, 6, and 12 months. CAN at 6 and 12 months was associated with reduced graft function (P = 0.001). Semiquantitative CADI scores at all time-points significantly correlated with glomerular filtration rate (GFR) at 18 months. Strongest correlation existed with CADI at 12 months (P < 0.001). Change in CADI between 0-6 and 0-12 months, but not between 0-3 and 3-12 months, correlated with GFR at 18 months (P = 0.03, P = 0.01). Subclinical rejections were rare and chronic changes mild at 3 months. In our well-matched population, the predictive value of a biopsy at 3 months was inferior to biopsies at 6 or 12 months, both of which were effective in predicting long-term graft function.