BACKGROUND. The performance of two commercially available detection systems for high-risk HPV (hrHPV), Hybrid Capture 2 (HC2) and in situ hybridization (ISH), were compared on cervical scrapings. METHODS. Using general primer (GP)-mediated GP5+/6+-polymerase chain reaction (PCR)-enzyme immunoassay and reverse line blot genotyping, 76 liquid-based cervical samples were identified with ≥ 1 of the 12 hrHPV types present in the probes of the HC2 and ISH assays. The positivity rate of the assays and the HC2 viral load were determined and related to cytologic findings (n = 76 samples) and histologic findings (n = 43 samples). RESULTS. Overall, HC2 scored significantly more samples positive compared with ISH (P < 0.01). Seventy-four of 76 samples (97%) were positive according to HC2. Forty-six of 76 samples (61%) were positive according to ISH, including 80% and 70% of samples that were classified cytologically as moderate dysplasia and severe dysplasia, respectively. All women with underlying cervical intraepithelial neoplasia (CIN) lesions and 67% of women without CIN had positive HC2 samples. ISH scored 33%, 66%, 88%, and 73% of samples positive of women with no CIN, Grade 1 CIN (CIN 1), CIN 2, and CIN 3, respectively. The HC2 viral load was significantly higher in women who had a cytologic diagnosis of dysplasia (P < 0.01) and in women who had an underlying diagnosis of CIN (P < 0.01) compared with women who had neither. In addition, the viral load was significantly higher in ISH positive samples compared with ISH negative samples (P < 0.01). CONCLUSIONS. An increased HC2 viral load was associated with an increased chance of underlying high-grade CIN disease in women who tested hrHPV GP5+/ 6+-PCR positive. Moreover, although positive ISH results were associated with an increased overall viral load in the sample, the analytic sensitivity of ISH was too low to detect all women with prevalent high-grade CIN.