The cornea is one of the few human tissues where the in situ locations of stem cells (SCs), transient-amplifying (TA) cells and terminally-differentiated (TD) cells have been relatively well localised and characterised. Mid-infrared (IR) (4000-400 cm(-1)) is absorbed by biological molecules and facilitates the acquisition in the biochemical-cell fingerprint region (1800-900 cm(-1)) of spectra representative of structure and function. Human cornea derived from normal or squamous cell carcinoma (SCC) samples were acquired, cryosectioned (10 µm), floated onto BaF(2) windows and interrogated using synchrotron-based radiation (SRS) Fourier-transform IR (FTIR) microspectroscopy. Spectra were analysed using principal component analysis (PCA) with or without linear discriminant analysis (LDA) to allow cluster analysis of the cell categories. A clear cell lineage emanating from SCs to TA cells to TD cells was noted in normal samples. Within the SCC samples, a small sub-population of the cell-derived spectra pointed to a SC-like phenotype with the vast majority pointing to a TA cell-like character; these cells would tend to be the most proliferative within a tissue. Our findings suggest that SRS FTIR microspectroscopy has the potential to identify and characterise cancer SCs.