Human papillomavirus (HPV) testing using molecular methods in liquid based cytology (LBC) specimens may be useful as an adjunct to cervical screening by cytology. We compared the positivity rate of the commercially available HPV DNA method hybrid capture 2 (hc2) and the commercially available E6/E7 mRNA method PreTeCt (TM) HPV-Proofer in cytological specimens (n = 299).LBC specimens collected (n = 299) represented the following cervical cytological disease categories: Normal (n = 60), borderline nuclear abnormalities (BNA) (n = 34), CIN1 (n = 121), CIN2 (n = 60), CIN3 (n = 24). Overall, 69% (205/299) of the cases were positive by hc2 and 38% (112/299) of the cases were positive by PreTect (TM) HPV-Proofer. Concordance rates between the two tests were highest in the high-grade cytology cases (CIN2: 67% and CIN3: 83%) and the normal cytology cases (88%) and lowest in the BNA and CIN1 categories (56% and 52%). HPV DNA viral load analyses were carried out on HPV16 (n = 55), HPV18 (n = 9) and HPV33 (n = 13) samples that were positive by PreTect (TM) HPV-Proofer. The sensitivity and specificity of PreTeCt (TM) HPV-Proofer and the hc2 DNA test for the detection of high-grade cytology (i.e. CIN2+) were 71.4% and 75.8% vs 100% and 43.7%, respectively. The relatively low detection rate observed by PreTect (TM) HPV-Proofer in the whole range of cytological positive cases, combined with a relatively higher specificity and PPV. suggests that PreTeCt (TM) HPV-Proofer may be more useful than hc2 for triage and in predicting high-grade disease.