Abstract: Objective: OSCC is associated with poor prognosis, which has improved only marginally over the past three decades. A proteomic analysis of OSCC lesions may help identify novel molecular targets for the early detection, prevention, and treatment of it. Methods: Laser capture microdissection was combined with recently developed techniques for protein extraction from formalin-fixed paraffin-embedded (FFPE) tissues and a novel proteomics platform. Approximately 10,000 cells procured from FFPE tissue sections of normal oral epithelium and OSCC epithelium were processed for mass spectrometry and bioinformatic analysis. Results: A large number of proteins expressed in normal oral epithelium and OSCC, including cytokeratins, intermediate filaments, differentiation markers, and proteins involved in stem cell maintenance, signal transduction, migration, cell cycle regulation, growth and angiogenesis, matrix degradation, and proteins with tumor suppressive and oncogenic potential, were readily detected. Of interest, the relative expression of many of these molecules followed a distinct pattern in normal squamous epithelia and OSCC tumor tissues. Representative proteins were further validated basing on article reviews. CKs expression pattern may afford potential predict biomarkers for oral mucosa carcinogenesis. Conclusions: The ability to combine laser capture microdissection and in-depth proteomic analysis of FFPE tissues provided a wealth of information regarding the nature of the proteins expressed in normal squamous epithelium and during OSCC progression, which may allow the development of novel biomarkers of diagnostic and prognostic value and the identification of novel targets for therapeutic intervention in OSCC.