In vivo LIF spectroscopy and imaging, using 442 nm exc. light delineates normal from adenomatous colonic tissue. This study investigates the microscopic origin of the observed tissue autofluorescence differences using Confocal Fluorescence Microscopy (CFM), histological analysis, confocal microspectrofluorimetry and Monte Carlo simulation. A multilayered tissue model is developed for normal, flat and polypoid adenomas. based on: 1) tissue architecture, 2) optical properties, 3) fluorescence distribution, and 4) illumination/detection geometries. Major differences were found in fluorescence intensity and spectral lineshape between normal and adenomatous colon samples. Fluorescence spectral composition of normal and adenomatous colon autofluorescence is tissue depth-dependent for normal, premalignant, and malignant tissues. Mathematical modeling suggests that LIF measurements are primarily sensitive to changes in tissue morphology specific to pathological progression, including mucosal thickening, alteration in mucosal tissue constituents, redistribution of submucosal collagen and significantly increased blood volume.