Cytobrush samples of 80 patients, who previously had a cytological or histopathological diagnosis of condyloma and/or dysplasia were investigated for human papillomavirus infection (HPV) by polymerase chain reaction (PCR) and in situ DNA hybridization technique (ISH). The results were compared with concomitantly obtained cytological Pap-stained smears or, in some cases, histological sections. The time between the diagnosis of the original and the concomitant cytology/histopathology was less than 1 yr. Six additional patients had similar morphological diagnoses 2-4 yr before. Five more cases were included on clinical diagnosis of HPV. Compared with the original morphological diagnoses, 70% of the cases were positive by PCR and/or ISH. The concomitant morphology was not diagnostic of HPV in 44 out of 80 cases (55%), showing a relatively high percentage of cases morphologically normalized in the interval since the first specimen was taken. After detection with PCR, 30 cases (37.5%) were negative for HPV. Only one of the patients with a previous disease 2-4 yr before was HPV positive by PCR and two out of five patients with a clinical diagnosis of HPV. ISH could be performed on 67/80 cases, 43 of which were positive for HPV. There was a good agreement between the results of ISH and PCR, but there were six cases positive by ISH and negative by PCR. In these cases, few infected cells may have escaped detection by PCR. Both methods seem to be able to detect silent HPV infections and comparison with concomitant cytology/histopathology shows that morphology alone is insufficient for HPV detection in these cases.