To identify BKPyV, the VP1 protein sequence was analyzed and classified into genotypes in 246 RTRs before and after RTx from deceased donors during a one-year observation period. Quantitative assessment of BKPyV was conducted via qPCR. Prior to RTx, genotypes I and IV were identified in the urine (7.27 × 106; 1.20 × 105) and in serum (5.75 × 104; 1.12 × 104). After RTx, genotype I was predominant; identification of DNAuria-BKPyV (62.07%) and BKPyV-DNAemia (55.56%) peaked after three months, and the highest DNAuria-BKPyV titer was also observed after three months (6.48 × 109), whereas the BKPyV-DNAemia titer did not peak until after six months (2.21 × 107). The highest number of copies of genotype IV in the urine was observed after six months (9.54 × 109), while the highest titer in the serum was not observed until after 12 months (3.88 × 106). DNAuria-BKPyV precedes BKPyV-DNAemia, affects a larger group of patients, and has a greater and more easily detected viral load, which makes it not only an earlier marker, but the key predictive marker of greater clinical value than later detection of BKPyV-DNAemia alone. Early monitoring of DNAuria-BKPyV should be the basis of classical screening, and not merely an addition to it, and therapeutic interventions should be undertaken early to prevent nephropathy.