Cell-based biosensors rely on the detection and identification of single cells as well as monitoring of changes induced by interaction with drugs and/or toxic agents. Raman spectroscopy is a powerful tool to reach this goal, being non-destructive analytical technique, allowing also measurements of samples in aqueous environment. In addition, micro-Raman measurements do not require preliminary sample preparation (as in fluorescence spectroscopy), show a finger-print spectral response, allow a spatial resolution below typical cell sizes, and are relatively fast (few s or even less). All these properties make micro-Raman technique particularly promising for high-throughput on-line analysis integrated in lab-on-a-chip devices. Herein, we demonstrate some applications of Raman analysis in ophthalmology. In particular, we demonstrate that Raman analysis can provide useful information for the therapeutic treatment of keratitis caused by Acanthamoeba Castellanii (A.), an opportunistic protozoan that is widely distributed in the environment and is known to produce blinding keratitis and fatal encephalitis. In particular, by combining Raman analysis with Principal Component Analysis (PCA), we have demonstrated that is possible to distinguish between live and dead cells, enabling, therefore to establish the effectiveness of therapeutic strategies to vanquish the protozoa. As final step, we have analyzed the presence of biochemical differences in the conjunctival epithelial tissues of patients affected by keratitis with respect to healthy people. As a matter of facts, it is possible to speculate some biochemical alterations of the epithelial tissues, rendering more favorable the binding of the protozoan. The epithelial cells were obtained by impression cytology from eyes of both healthy and keratitis-affected individuals. All the samples were analyzed by Raman spectroscopy within a few hours from cells removal from eyes. The results of this analysis are discussed.