High-risk human Papillomaviruses (HR-HPV) - the most carcinogenic infectious agents - are responsible for the development of cervical cancer. The knowledge of HPV infection natural history and viral carcinogenesis led to the investigation of viral biomarkers (genotype, viral load, integration, E6/E7 mRNA expression, viral DNA methylation) from clinical samples representative of the evolution of cervical lesions. Mostly concerning HPV16, the literature data agree on an increase of viral load, proportion of samples harboring integrated HPV genomes and methylation of CpG located in the L1 gene with the lesion severity. Viral load and L1 CpG methylation are interesting for clinical practice since appropriate cutoff values allow the identification of precancerous lesions with a high specificity. Although HPV E6/E7 transcript detection is more specific than HPV DNA detection to identify precancerous cervical lesions, viral transcript quantitation and cutoff value determination are unlikely feasible in clinical practice. Taken together, data highlight promising biomarkers that could be integrated to screening algorithms.