Long-term exposure to high-risk human papilloma virus (HPV) leads to high grade squamous intraepithelial lesion (HSIL), which might develop into cancer. Various proteins and metabolites change during the development of cervical cancer, thus as-sessing the dysregulated molecules and pathways of HSIL is important to provide the diagnostic biomarkers. In proteomics analysis, 836 proteins showed significantly changes. Functional analyses of the differentially expressed proteins indicated that metabolic pathways, oxidative phosphorylation and ribosome are top three enriched pathways.