Purpose Recent studies used impression cytology with scanning electron microscopy (SEM) to study the conjunctival surface of bovine eyes and normal human eyes. The purpose of this study was to evaluate the use impression cytology and SEM (ICSEM) in patients affected by tear film abnormalities. Methods Forty-five patients were divided into three groups according to mild, moderate or severe subjective sensation of dry eye. Fifteen asymptomatic subjects served as control group. In all patients the tear film was evaluated with break-up time (BUT), Schirmer's, and Ferning test, whereas conjunctival epithelium was evaluated with impression cytology and optic microscopy (ICOM), and ICSEM. The Spearman rank correlation test was used to compare the outcome of these examinations with the subjective sensation of dry eye in each group, and to identify correlations among the five tests. Results ICSEM findings highly correlated with subjective dry eye sensation (Spearman correlation coefficient, 796; Po0.01). ICSEM revealed incipient epithelial damage (reduction or absence of microvilli) before the appearance of alterations of nucleus and cytoplasm of epithelial cells revealed by optic microscopy. The number of microvilli was correlated with the degree of tear film abnormalities and subjective sensation of dry eye (Spearman correlation coefficient, 796; Po0.01). Conclusion ICSEM was very effective in detecting the reduction in the number of microvilli. Therefore, it could represent an effective method to detect alterations in the conjunctival epithelium resulting from tear film damage even before the epithelial damage occurs and is detected by optic microscopy.