This study aimed to evaluate whether quantitation of high-risk human papillomavirus (HR-HPV) E6 messenger RNA (mRNA) can be a potential biomarker for detecting the severity of cervical lesions. HPV genotyping was performed using a modified MY11/GP6+ PCR for HPV DNA amplification, followed by HPV genotype-specific hybridization with on a gene chip. E6 type-specific PCR was used to validate multiple infections. Quantitative real-time reverse transcriptase (QRT-PCR) and real-time PCR used to measure mRNA levels and DNA viral loads of 6 HPV oncogenic types (HPV 16, 18, 31, 33, 52 and 58) in 720 liquid-based cytology samples. The HPV DNA and RNA measurements were correlated with cervical lesions diagnosed by histopathologic examination. mRNA transcripts in the 6 types HPV DNA-positive cases was lower in normal women and <CIN 1 (23%), women with CIN 1 (54%), CIN2+ (77%) and CIN3+ (80%) (p < 0.001). Geometric mean mRNA levels ranged from 24.5 (copies per 50 ng total RNA) in normal women and <CIN 1 to 210.8 in those with CIN 1, 629.0 in CIN2+ and 699.0 in CIN3+ (p < 0.0001). Trends of increasing viral mRNA with severity of histopathologic diagnosis were significant for HPV 16, 18, 52 and 58 transcripts but not for HPV 31 and 33 transcripts. However, geometric mean DNA viral loads of HPV 16, 18, 52 and 58 DNA did not significantly increase with the severity of cervical dysplasia. Therefore, quantitative HPV E6 mRNA levels of high-risk HPV types are potentially useful biomarkers for distinguishing among HPV infections, cervical precancerous lesions and cancer.