Noninvasive detection of BK virus, for early detection of BK polyomavirus-associated nephropathy post-renal transplantation, is currently an active subject of investigation. In this study, we developed and validated a novel risk score diagnostic assay (PymiR Score) based on measurements of three urine miRNAs, including BKV-related miRNA (bkv-miR-B1-5p), polyomavirus-related miRNA (bkv-miR-B1-3p) and renal tubular injury-related miRNA (miR-21-5p), by quantitative polymerase chain reaction. The limit of detection of the three miRNAs was 2 × 10