It has been suggested that human papillomavirus (HPV) testing improves follow‐up of atypical cells of undetermined significance (ASCUS) and low‐grade squamous intraepithelial lesion (LSIL) in cervical cancer screening programs. To evaluate the prognostic value of including HPV testing as an adjunct to cytology, we carried out a 2‐year follow‐up study of 77 women with ASCUS or LSIL Papanicolaou (Pap) smear in the Norwegian Cervical Cancer Screening Program (NCCSP) for detection of histological cervical intraepithelial neoplasia (CIN) 2+. The study includes a comparison between viral mRNA and DNA detection. PreTect HPV‐Proofer was used for HPV E6/E7 mRNA detection from the 5 high‐risk types 16, 18, 31, 33 and 45, and Gp5+/6+ consensus PCR was used for HPV DNA detection. Twice as many women were positive for HPV DNA (54.6%) than for HPV mRNA (23.4%). PreTect HPV‐Proofer and consensus PCR had a sensitivity of 85.7% (95% confidence interval CI = 42.1–99.6) for detecting CIN2+ during follow‐up. The specificity was significantly higher for PreTect HPV‐Proofer, 84.9% (95% CI = 73.9–92.5), than for consensus PCR, 50.0% (95% CI = 37.4–62.6). PreTect HPV‐Proofer positive women were 69.8 times (95% CI = 4.3–1137.3) more likely to be diagnosed with CIN2+ within 2 years than PreTect HPV‐Proofer negative women. Consensus PCR‐positive women were 5.7 times (95% CI = 0.6–52.0) more likely to be diagnosed with CIN2+ within 2 years than PCR‐negative women. With equal sensitivity and higher specificity than consensus PCR, the PreTect HPV‐Proofer might offer an improvement for the triage of women with ASCUS or LSIL Pap smear. © 2004 Wiley‐Liss, Inc.