PURPOSE. High-resolution synchrotron radiation-based Fourier transform infrared (SR-FTIR) microspectroscopy coupled with multivariate analysis was used to investigate the characteristics of putative adult stem cell (SC), transiently amplified (TA) cell, and terminally differentiated (TD) cell populations of the corneal epithelium. METHODS. Spectra of individual cells in situ in cryosections of bovine cornea were collected by using a synchrotron microspectroscopy facility at Daresbury Laboratory (United Kingdom). The resultant spectra were analyzed by multivariate analysis. RESULTS. The median spectra of the three different cell populations showed marked differences, which correlated with their degree of differentiation and proliferative capacity. Multivariate (principal component) analysis (PCA) showed that the three cell populations could be segregated into discrete clusters, with only a slight overlap between the SC and TA cell populations. Further analysis (Mann-Whitney test) indicated that the most significant (P