The relevance of viral infections in the development of allograft lesions is still unclear, although some viruses have been implicated. The present study investigated systemic and intrarenal viral infections in kidney transplant recipients and their association with the risk of acute rejection and chronic allograft injuries that are predictive of long-term dysfunction. The presence of DNA sequences of human herpesviruses, polyomaviruses, and parvovirus B19 was analyzed in renal allograft biopsy specimens obtained at baseline, after acute renal dysfunction, and during follow-up evaluation in 69 transplant recipients who were children or young adults. Results were correlated with clinical data, viral DNAemia, and results of renal function tests and allograft histology analyzed at the same time points. Overall, viral DNA was detectable in 46% of baseline and 70% of follow-up biopsy specimens of kidney allografts, where it generally persisted. The most frequently detected viruses were B19 and human herpesvirus 6, already present in donor kidneys, and BK virus and Epstein-Barr virus, usually involving the allograft during follow-up. Among viruses, only the intrarenal persistence of B19 DNA and B19 DNAemia was associated with the development of chronic allograft injury, whereas human cytomegalovirus DNAemia was a risk factor for acute rejection. Parvovirus B19 seems to target the kidney electively. Its intrarenal persistence is associated with chronic kidney allograft injury.