Flow cytometry (FCM) is a widely used technique, not only in immunology and hematology but also in many other domains and new applications have been developed in ophthalmology, for investigating ocular surface biology and pathophysiology. Apoptosis, proteins specific of cell lineage, expression of activation or immune-related markers, proinflammatory cytokine production, multi-drug resistance and oxidative stress are some examples of possible pathways that may be explored directly using ocular surface cells removed with the non-invasive technique of impression cytology, by means of flow cytometry. Conjunctival cells are thus collected by impression cytology on a filter, fixed in paraformaldehyde and dissociated by agitation before immunostaining and FCM processing. Important observations have been made concerning Sjögren's syndrome, ocular allergy and antiglaucoma eye drop toxicity. Studies performed on impression cytology with FCM techniques confirmed inflammatory and apoptotic patterns in a large number of patients with keratoconjunctivitis sicca or receiving long-term treatments with antiglaucoma drugs, even though they did not present any clinical signs of inflammation. FCM may now be used for large multicenter clinical trials and has already contributed to a better understanding of ocular surface pathophysiology, the monitoring of new immunomodulating drugs and knowledge concerning topical drugs, as regards both efficacy and safety.