A human papillomavirus (HPV) microarray system allows the determination of HPV type in clinical samples. The purpose of this study was to determine the presence of HPV in liquid-based Pap smears with the MyGene MyHPV Chip Kit HPV genotyping microarray test (MyGene Assay), and to correlate this with the cytology and biopsy diagnoses, clinical follow-up, HPV Hybrid Capture data, and HPV sequence analyses. Four hundred and two Pap smears (93 ThinPrep, 309 SurePath) were available for study. Correlation of HPV DNA detection by the MyGene Assay with the Pap smear diagnosis showed a detection rate of 19/97 (19%) for normal Pap smears, 181/242 (74%) for atypical squamous cells of undetermined significance (ASCUS), and 61/63 (97%) for squamous intraepithelial lesions (SILs). Biopsy data on 248 women were available. HPV was noted by the MyGene Assay in the Pap smear in 98/100 (98%) of the cases, for which the corresponding biopsy had been diagnosed as SIL, compared with 103/148 (69%) of the cases for which the biopsy had been negative for SIL. Clinical follow-ups were available for 200 women with ASCUS Pap smears. A significant increase was observed in the rate of biopsy-proven SILs in women with ASCUS Pap smears that were HPV-positive (63/66=95%) as compared with those that were HPV-negative (96/134=71%, P<0.05). The MyGene Assay and Hybrid Capture system gave equivalent results for all the categories studied, except for the presence of multiple infections, as determined by viral sequence analysis. Specifically, the Hybrid Capture system overestimated the presence of dual infection (low-risk and high-risk positive) by 48% and missed many cases of multiple infections, especially when 2 or more high-risk types were present. It is concluded that the MyGene Assay allows for the routine typing of HPV in liquid-based Pap smears, and that the presence of HPV DNA in ASCUS Pap smears is strongly correlated with a biopsy-proven SIL.