Distribution of various types of genital human Papillomavirus (HPV) in smears from histologically classified cervical lesions was determined by hybrid capture assay (HCA) and was compared with a polymerase chain reaction (PCR) system using general primers (GP) in first and type specific primers (TS) in a second step. The overall agreement of high-risk HPV by HCA and the more sensitive GP/TS PCR was 80.6% (204 of 253, kappa value 0.6). Human Papillomavirus frequency by GP/TS PCR was 14–20% higher compared with HCA (p = 0.02–0.004) independent of morphology. Only one sample was positive by HCA and negative by GP/TS PCR. A significantly higher frequency was found using HCA and GP/TS PCR in smears from histologically proven cervical intraepithelial lesions (CIN) II/III compared with CIN I, tissues with minimal changes (metaplasia, cervicitis, or lack of glycogenization), or normal morphology (61% and 81% vs 8–15% and 24–34%, p ≤ 0.001). Semi-quantitative estimate of HPV DNA copies by GP-PCR coincided with estimated virus load by quantitative HCA and was significantly higher in patients with CIN II/III compared with CIN I (p < 0.001). Thus, the GP-PCR may be used to monitor the amount of HPV DNA copies in clinical samples. A direct correlation between morphologic changes and HPV detection as well as virus load was found by HCA and the more sensitive GP/TS PCR.