The aim of this study was to compare the ability of two methods, the polymerase chain reaction (PCR) and cervical cytology, to detect HPV infection. The study population included 222 randomly selected women without dysplasia (controls) and 91 women with histologically confirmed dysplasia (CIN II-III) (cases). In women without dysplasia, 8.6% had cytological signs of HPV infection, whereas 15.3% were HPV DNA positive by PCR. In women with dysplasia, 72.5% had cytological signs of HPV infection, whereas 90.1% were HPV PCR positive. The statistical agreement between the two diagnostic methods was low (controls: kappa = 0.26, cases: kappa = -0.03). In total, PCR failed to detect 17 of 85 women with cytological signs of HPV infection, whereas cervical cytology failed to detect 48 of 116 HPV PCR-positive women. In women with dysplasia, but not in women without dysplasia, the oncogenic HPV types were associated with cytological signs of HPV infection.