A small percentage of renal patients become infected with the BK polyomavirus (BKV), a pathogenic virus that causes BKV-associated nephropathy (BKVN), after kidney transplantation. This study presents a simple, rapid, high-throughput method for BKV genotyping using high-resolution melt analysis (HRMA). Using this novel method, BKV genotypes were analyzed in 49 samples taken from BKV-positive renal transplantation patients for classification into 1 of 3 genotypes: GI-1 (subgroups Ia, Ib1, and Ic), GI-2 (subgroup Ib2), and GII-IV (subtypes II, III, and IV). HRMA was performed to compare each sample sequence to a reference sequence that contained a combination of 2 of the 3 genotype groups, and the findings validated by conventional DNA sequencing. Of the 49 samples, 20 samples were classified as GI-1, 18 as GI-2, and 11 as GII-IV, suggesting that the predominant BKV strain (77.6%) in these patients was subtype I (GI-1 and GI-2). The HRMA method presented here is a time-saving, reliable, and low-cost procedure that can be developed as a diagnostic tool in the detection of the specific BKV genotypes associated with BKVN. J. Med. Virol. 83:2128–2134, 2011. © 2011 Wiley Periodicals, Inc.