Background Recently, the QPLEX™ human papillomavirus (HPV) genotyping kit (QuantaMatrix, Seoul, Korea), a Microdisk™ technology-based multiplex system, was developed to detect 32 HPV genotypes. We evaluated the analytical performance of this kit by conducting a comparison study, precision evaluation and interference testing. Methods A total of 1594 cervical swab specimens were used to compare the QPLEX™ HPV genotyping kit with other commercially available kits (GeneFinder HPV Liquid Bead MicroArray Genotype polymerase chain reaction [PCR] kit, Infopia, Seoul, Korea; PANArray™ HPV Genotyping Chip, PANAGENE, Daejeon, Korea). For the determination of precision, we evaluated four types of precision profiles: repeatability, lot-to-lot variability, operator-to-operator variability and site-to-site variability. In addition, interference tests were performed with various interferents. Results The results of the QPLEX™ HPV genotyping kit showed almost perfect agreement with the other commercially available HPV genotyping assays. The combined precision was acceptable. In addition, there was no tested interferent that affected the results of the QPLEX™ HPV genotyping kit. Conclusions The QPLEX™ HPV genotyping kit showed acceptable analytical performance in our study. This assay could be a suitable option for HPV genotyping in routine and follow-up tests.