Abstract Autofluorescence spectroscopy and Raman spectroscopy have been suggested for lesion diagnostics. We investigate the information contained in autofluorescence and Raman spectra recorded from oral tissue slices of various lesion types. Thirty-seven human oral mucosa lesions were biopsied and freeze-dried. Complete autofluorescence images and spectra were recorded from 20 m sections. Raman spectra were acquired from the same positions for 12 of the sections. Cluster analysis was applied to find any relationship between spectral shape and lesion type or cell layer. Autofluorescence images showed high intensities for keratin layers and connective tissue, but hardly any for the epithelium. Autofluorescence spectra were centered around 520 nm and did not show specific spectral features. No clustering with regard to lesion type or cell layer was observed. Raman spectra allowed for reliable classification into cell layers, but differences between lesion types were not significant in this study. Autofluorescence spectra of freeze-dried oral mucosa sections did not contain useful information. A more comprehensive study is required for Raman spectra. Keywords Autofluorescence microspectroscopy - Raman microspectroscopy - Ex vivo - Oral cancer - Oral leukoplakia - Oral pathology@en