The study documents histopathologic outcomes and high-risk (hr) human papillomavirus (HPV) test results in a large cohort of patients with high-grade squamous intraepithelial lesion (HSIL) liquid-based cytology (LBC) Pap test results. A total of 352 patients with HSIL results (338 cervical and 14 vaginal) who had hrHPV testing and 290 patients with biopsy follow-up were studied. hrHPV detection rates were compared at different ages, with or without an endocervical/transformation zone sample (EC/TZS), and for cervical and vaginal HSIL Pap smears. Histopathologic follow-up findings were also compared. hrHPV-negative HSIL slides were re-evaluated in a blinded manner. A total of 325 of 338 (96.2%) cervical HSIL and 12 of 14 (87.5%) vaginal HSIL tested hrHPV-positive. A total of 271 of 281 (96.4%) EC/TZS-positive cervical HSIL and 54 of 57 (94.7%) EC/TZS-negative cervical HSIL tested hrHPV-positive. The percentage of hrHPV-positive HSIL declined slightly with increasing age. 197 of 273 (72.3%) hrHPV-positive cervical HSIL had histopathologic cervical intraepithelial neoplasia (CIN) 2/3+ follow-up, including 8 squamous carcinomas, compared with 4 of 12 (33.3%) hrHPV-negative HSIL with CIN2/3 (no carcinomas). 167 of 241 (69.2%) EC/TZS-positive HSIL had CIN2/3+ follow-up, compared with 34 of 44 (77.3%) EC/TZS-negative HSIL. Equivocal HSIL morphology characterized some HPV-negative HSIL without CIN2/3+ follow-up. hrHPV was detected in LBC vials from 96.2% of 338 cervical HSIL and 85.7% of 14 vaginal HSIL. CIN2/3+ was significantly more likely with hrHPV-positive cervical HSIL than with hrHPV-negative cervical HSIL. Presence or absence of an EC/TZS did not significantly impact HSIL hrHPV or CIN2/3+ rates. Some hrHPV-negative HSIL cases may represent HSIL cytologic mimics.