Concerning the prediction of HPV-associated cervical disease, several importance issues are related both to the management of women with diagnosed CIN and those with cervical cancer. Oncogenic HPVs are capable of contributing to the development of malignant phenotype by several different mechanisms, most of which seem to be closely interrelated. Because of the fact that these molecular interactions are mediated by proteins, the logical strategy to dissect the complex molecular pathways is to study the functions of these proteins, utilising the capabilities of immunohistochemistry (IHC). IHC offers practically unlimited possibilities to study any target molecules, against which a monoclonal or polyclonal antibody can be raised. This review describes the IHC-based strategies used by this author to assess the molecular pathogenesis of cervical cancer and its precursors in a number of large-scale prospective cohort studies conducted during the past 25 years. In the ongoing HPV-PathogenISS study, 13 different markers are being tested to evaluate their predictive value in distinct viral events, e.g. persistence or clearance of high-risk HPV in women treated for CIN. Apart from getting new insights into the molecular pathogenesis of HPV-associated cervical carcinogenesis, we anticipate the disclosure of individual markers, a set of markers, or an expression profile of any such marker sets that would be of clinical value as predictors of disease outcome in cervical carcinogenesis.