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Fluorescence spectroscopy of tissue is a promising technique for early detection of precancerous changes in the human body. Investigation of the microscopic origin of the clinically observed tissue fluorescence can provide valuable information about the tissue's histology. The objective of this study was the development of a morphological model of colon tissue fluorescence which connects the clinically observed spectra with their underlying microscopic origins. Clinical colon tissue fluorescence spectra were modeled by measuring the intrinsic fluorescence properties of colon tissue on a microscopic level and by simulating light propagation in tissue using the Monte-Carlo method. The computed spectra were in good agreement with the clinical spectra acquired during colonoscopy, and exhibited the characteristic spectral features of the in vivo collected spectra. The authors' analysis quantitated these spectral features in terms of the intrinsic fluorescence properties of tissue and its general histological characteristics. The fluorescence intensity difference between normal and adenoma observed in vivo was found to be due to the increased hemoglobin absorption, the reduced mucosal fluorescence intensity, and the absence of submucosal fluorescence in adenomatous polyps. The increased red fluorescence in adenoma was found to be associated with the dysplastic crypt cell fluorescence.