The identification of stem cells in adult tissue is a challenging problem in biomedicine. Currently, stem cells are identified by individual epitopes, which are generally tissue-specific. The discovery of a stem cell marker common to other adult tissue types could open avenues in the development of therapeutic stem cell strategies. We report the use of the novel technique of Fourier transform infrared near-field photothermal micro-spectroscopy (FTIR-PTMS) for the characterization of stem cells, transit amplifying (TA) cells and terminally differentiated (TD) cells in the corneal epithelium. Principal component analysis (PCA) data demonstrates excellent discrimination of cell type by spectra. PCA in combination with linear discriminant analysis (PCA-LDA) shows that FTIR-PTMS very effectively discriminates between the three cell populations. Statistically significant differences above the 99% confidence level between infrared (IR) spectra from stem cells and TA cells suggest that nucleic acid conformational changes are an important component of the differences between spectral data from the two cell types. FTIR-PTMS is a new addition to existing spectroscopy methods based on the concept of interfacing a conventional FTIR spectrometer with an atomic force microscope equipped with a near-field thermal sensing probe. FTIR spectroscopy currently has a spatial resolution which is similar to that of diffraction-limited optical detection FTIR spectroscopy techniques, but as a near-field technique has considerable potential for further improvement. Our work also suggests that FTIR-PTMS is potentially more sensitive than synchrotron radiation FTIR spectroscopy for some applications. Micro-spectroscopy techniques like FTIR-PTMS provide information about the entire molecular composition of cells, in contrast to epitope recognition which only considers the presence or absence of individual molecules. Our results with FTIR-PTMS on corneal stem cells are promising for the potential development of an IR spectral fingerprint for stem cells.