The number of end stage renal failure patients receiving hemodialysis or peritoneal dialysis in Taiwan is on the increase. Of the various treatment options, kidney transplantation is considered to be the ultimate choice, however, it may lead to certain complications, including the infection or reactivation of the BK virus (BKV). Such viral complications may cause nephritis of the donated kidney and eventually dysfunction and transplantation failure. Therefore the early detection of BKV may be beneficial for kidney transplant recipients. The aim of the present study was to demonstrate the impact of BKV infection on renal function and to show the feasilibility of urine qualitative polymerase chain reaction (PCR) as a screening test in renal transplantation patients. A total of 250 patients were screened for the presence of BKV or John Cunningham virus (JCV) DNA in the urine via qualitative PCR. Subjects positive for urine screening were then further tested using blood sampling. The results showed that 16 patients (6.4%) were co‑infected by BKV and JCV with a prevalence of 20.4 and 38.4%, respectively. The correlations between viral infection and renal function were further analyzed to show that an infection of BKV has significant effects on the serum creatinine concentration. The mean serum creatinine concentration of the BKV‑positive patients was 1.39±0.09 mg/dl, which was significantly higher than that of the BKV‑negative patients (1.21±0.03 mg/dl; P<0.05). However, JCV infection has no such effect on renal function. Taken together, these results suggested that PCR monitoring of BKV with urine samples is a rapid, non‑invasive and beneficial method for the prevention of renal complications during the long‑term care of kidney transplant recipients.