Human papillomavirus types 16 and 18 (HPV 16/18) are considered to play an important role in the pathogenesis of cervical intraepithelial neoplasia (CIN) and invasive cancer of the uterine cervix. The in situ hybridization (ISH) is the only method demonstrating a correlation between histopathological findings and the presence of specific HPV DNA, but its sensitivity is limited. To determine whether or not the mode of sample taking contributes to the reported HPV prevalence with this method two observers examined the cervical swabs and tissue sections of 41 CIN lesions independently with the same commercial ISH kits (PathoGene/Enzo Diagnostics Inc., New York). HPV prevalences were almost identical in both sample groups (21/41 HPV positive tissue sections and 23/41 HPV positive swabs). 30/41 samples (73%) showed identical HPV-ISH results in the biopsy and the corresponding swab. There was only one CIN 1 lesion with different associated HPV types in the corresponding tissue section and cervical swab. By accumulating the results of both sample groups 27 out of 41 CIN lesions had either an HPV positive swab or biopsy or both. The percentage of HPV 16/18 positive samples increased with the severity of the associated lesion.