BK virus associated nephropathy (BKVAN) in transplanted kidney, although recognized as a distinct entity in the 1970-es, continues to represent a challenge in kidney transplantation, mainly because the optimal treatment approach has not been determined yet. The fact that about 10-20% of patients have simultaneously some stage of acute rejection, complicate the treatment even more. Herein we present a case of BK nephropathy in the patient, one year after combined liver and kidney transplantation, complicated by episode of acute T-cell mediated rejection. Identification of decoy cells by cytology urine exam in patient with acute kidney graft function deterioration, raised suspicion of BKVAN. Diagnosis has been made by histological examination and confirmed with immunohistochemical staining for BK virus in kidney graft biopsy. One month after he had been treated for BKVAN with intravenous immunoglobulin, leflunomide and overall immunosuppression therapy reduction, there was further deterioration of graft function due to an episode of acute T-cell mediated rejection (Banff classification IA). He received 500 mg of metilprednisolon intravenously and mycophenolate mofetil had been reintroduced, which resulted in slow partial recovery of the graft function, but never to the baseline values. For the past two years his renal graft function has been stable, maintaining lower levels of immunosuppressive therapy. According to our knowledge this is the first documented case of BK virus associated nephropathy, diagnosed and confirmed with immunohistochemical staining of tissue from kidney biopsy in Croatia.