Infection with high-risk human papillomavirus (HPV) increases the likelihood of developing cervical cancer (CC). A plethora of cellular processes is required to produce pre-malignant lesions, which in turn may become malignant if left untreated. Those changes are induced by viral oncoproteins, which represent an ideal target to identify the viral presence, or by some particularities of the host that ultimately promote the establishment of CC. This article describes the different methods used for HPV detection and quantification, as well as the current trend of secondary screening approaches to detect premalignant lesions and CC. In addition, we analyzed validated biomarkers and those under clinical investigation for the classification (triage) of women at risk of developing CC after an initial positive HPV test and that could be used as prognostic biomarkers for CC. The use of molecular biomarkers, together with the detection of HPV DNA sequences, provides a high impact diagnostic and prognostic tool in the detection of patients at increased risk of developing CC and also may guide their clinical management. In addition, some of those biomarkers could represent pharmacological targets for the future design of therapeutic approaches to CC treatment.