The use of autofluorescence technique in the characterization of the sequential tissue transformation process in 7,12-dimethylbenz(a)anthracene and 12-O-tetradecanoylphorbol-13-acetate (DMBA & TPA) induced two-stage mouse skin carcinogenesis model in conjunction with a suitable statistical method is being explored. The fluorescence excitation emission matrix (EEM) from experimental group (n=40; DMBA/TPA application), control group (n=6; acetone application) and the blank group (n=6; no application of DMBA/TPA or acetone) were measured every week using Fluoromax3 spectrofluorometer coupled with a waveguide fiber optic bundle (JY Horiba, NJ). The EEM was recorded for 19 excitation wavelengths from 280 to 460 nm at 10 nm intervals and the fluorescence emission was scanned from 300 to 750 nm. During the tissue transformation the epithelial tissues underwent biochemical and structural changes that are manifested in the tissue fluorescence. To correlate the tissue morphology with the observed fluorescence differences in the fluorescence emission, animals were sacrificed and the tissue biopsies were subjected to histopathological evaluation. The fluorescence emission corresponding to different fluorophores was extracted from the EEM, and the spectral data were used in multivariate statistical algorithm for the earliest diagnosis of the onset of tissue transformation. The intrinsic fluorescence from tryptophan, NADH and prophyrins showed distinct differences in the spectral signature during the tissue transformation, due to the altered metabolic activities of the cells. The statistical analysis of the spectral data corresponding to each excitation wavelength showed better classification accuracy at 280, 320, 350 and 405 nm excitations, corresponding to tryptophan, collagen, NADH and porphyrins with the classification accuracy of 74.3, 68.1, 64.6 and 74.7 % respectively. The variations in the spectral signature and the results of the statistical analysis suggest that porphyrins, tryptophan and NADH can be targeted as potential tumor markers in the early detection of the tissue transformation process.