To examine the diagnostic utility for squamous intraepithelial lesion (SIL) by cytological in situ hybridization (c-ISH) for the human papillomavirus using liquid-based cytology specimens, we investigated c-ISH signal patterns in the cases of low-grade SIL (LSIL), atypical squamous cells of undetermined significance (ASC-US), and high-grade SIL (HSIL). Episomal (E) and/or integrated (I) signals were observed. Two signal patterns (E≧I or I>E) were obtained by counting the number of E+ or I+ cells. E≧I was specific to LSIL and ASC-US (10/12); I>E, to HSIL (9/11) (P<0.01, χ2 test), suggesting significant utility of c-ISH in diagnosing SIL. In the cell fraction, E≧I in large cells was dominant in LSIL. Two cases of I>E in large cells of LSIL showed HPV persistence and/or progression during follow-up. Thus, c-ISH is useful in routine testing for diagnosing cervical dysplastic lesions, especially for detecting LSIL suspected for progression.