The aim of this study was to examine the efficacy of semi-quantitative polymerase chain reaction (PCR) testing in cervical smears as an adjunct to cytological surveillance in a cohort of women with mild or moderate dyskaryosis. The study population comprised a group of 62 women who underwent twelve months of cytological and colposcopic surveillance as part of a larger randomised prospective study of women with mild and moderate dyskaryosis. Semi-quantitative PCR for HPV-16 DNA was carried out on the initial and twelve month study smears before a large loop excision of the transformation zone (LLETZ) was carried out. Smears from a control population which comprised 167 women without a history of abnormal cervical cytology who were attending family planning and general practitioner clinics for routine cervical smears were tested similarly. The presence of high or intermediate levels of HPV-16 DNA on both the initial and twelve month study smear was positively associated with the identification of cervical intraepithelial neoplasia (CIN) grades II or III in the LLETZ specimen (P = 0.01). While the combination of HPV-16 DNA testing with cytology on a repeat cervical smear improved the selection of women with underlying CIN II/III, there was still a false negative rate of 53%. Twenty-nine women had 'low risk' levels of HPV-16 DNA and mild dyskaryosis or less on both repeat smears indicating suitability for surveillance, but in fact 34% of them had CIN II/III. This study supports the finding reported previously of an association between high and intermediate levels of HPV-16 DNA and CIN II/III.(ABSTRACT TRUNCATED AT 250 WORDS)