A 10-year-old boy kidney transplant recipient (KTR) developed an abdominal post-transplant lymphoproliferative syndrome (PTLD) followed by BK virus nephropathy (BKVN). BK virus (BKV) and Epstein-Barr virus (EBV) were studied in renal and PTLD tissue by polymerase chain reaction (PCR) assay. Afterwards, the patient was monitored in relation to BKV in urine and serum; transcription control region (TCR)-BK polymorphism sequence analysis was also performed. In the PCR assay, both early large T antigen (LT) and late (VP1) transcriptional BKV coding regions were found in renal tissue, whereas EBV and only LT-BK were detected in PTLD abdominal tissue. On the other hand, TCR sequence analysis revealed the AS genomic BK variant.