Acute tubular injury (ATI) is commonly observed in renal allografts, especially early after transplantation. This study analyzes prevalence and associated clinical conditions of ATI in serial protocol biopsies (pBx) and indication biopsies (iBx), and its impact on long-term graft function. 612 pBx from 204 patients taken at 6 weeks, 3 and 6 months, and 151 iBx performed within the first year of transplantation were evaluated. Prevalence of ATI in pBx was 40% (6 weeks), 34% (3 months) and 37% (6 months), and 46% in iBx. ATI was associated with delayed graft function and prolonged cold ischemia time in pBx, and with acute rejections in iBx. The GFR at 1 and 2 years after transplantation correlated inversely with the frequency of ATI in both pBx and iBx (p < 0.001). Prevalence of chronic changes at 6 months was not significantly related to ATI (patients without ATI: 36%, patients with multiple ATI findings: 54%). ATI is linked to inferior long-term graft function. While this suggests lack of recovery from ATI with permanent allograft damage, the underlying molecular mechanisms need yet to be uncovered. Prevention of the potential pathogenetic factors identified in this study might be the key point to attain good long-term graft function.