Implementation of an optical clearing technique, called the Passive Clarity Technique (PACT), in mouse tongues enables three-dimensional (3D) fluorescence imaging of intact oral epithelial tissue. Using 3D imaging to improve our understanding of the spatial and temporal patterns of biomarker expression and phenotypic features in oral pre-cancer can improve accuracy of early diagnostic tools. Current methods for 3D fluorescence imaging require thin sectioning and accurate image reconstruction or are limited in imaging depth by tissue scattering. Using a polymer-tissue hydrogel technique previously developed for brain tissue, light scattering molecules were removed from mouse tongues to improve tissue transparency and antibody permeability for imaging and immunolabeling. In this study, PACT-Cleared tongues resulted in resolution of tissue features up to 500 μm in depth, while preserving tissue architecture and molecular information in normal and precancerous tissue. These findings can facilitate further exploration of biomarkers of oral cancer progression in a mouse model.