Embodiments of the invention provide methods, assays, and kits for detecting HPV infection, including infection by various HPV genotypes, early and/or late HPV-associated or HPV-specific proteins or antibodies. Detection of HPV DNAs, genomes, and/or oncoproteins by protein chips immunological assays can be used in early clinical screening for HPV infection and general diagnosis for cervical cancer and can be advantageous performed in a multiplexed test. Comparative detection of altered levels of HPV proteins and host proteins can performed in one or more assays. The polypeptides, recombinant proteins, antibodies, nucleic acids, and various detection methods thereof are particularly useful for diagnosing carcinomas of the uterine cervix and those at risk of developing cervical cancer.