We have previously demonstrated that cross-hybridization between probe and target occurs in the analysis of human papillomavirus (HPV) 6 and 11, and HPV 16, 31 and 33 infection by in situ hybridization (ISH) in archival tissue biopsies. In this study, 50 low grade and 50 high grade cervical lesions were analyzed using HPV 6/11, 16, 18, 31 and 33 probes to determine the typing accuracy of high sensitivity ISH for a wide range of HPV types. The sensitivity of both ISH and PCR was 92% in low grade lesions and 90% and 96%, respectively, in high grade lesions, with an overall concordance of 97%. The typing accuracy of ISH was only 43% in low grade lesions but 93% in high grade lesions. This was due largely to cross-hybridization of the probes used with other HPV types (HPV 39, 42, 43, 44, 45, 51, 52, 56, 58, and 66). Although analysis of ISH patterns could narrow down these other HPV types, precise identification was not possible by this means. These data suggest that when high sensitivity ISH methods are used, particularly in low grade lesions, HPV typing by ISH should be supplemented by independent determination of HPV type by PCR.