<jats:p><jats:bold>Aims: </jats:bold> Allergic eye disease affects up to 20% of the population with varying severity. The conjunctival epithelium plays a key role in allergic eye disease. The purpose of this study was to determine whether the conjunctival epithelium is abnormal in allergic eye disease.</jats:p><jats:p><jats:bold>Methods: </jats:bold> Conjunctival biopsy samples were taken from patients with seasonal allergic conjunctivitis (SAC) ‘in’ and ‘out of season’ and nonatopic control subjects. Specimens were fixed in glycol methacrylate, 2 <jats:italic>μ</jats:italic>m serial sections cut and Image‐J used to assess the sites and areas of immuno‐staining.</jats:p><jats:p><jats:bold>Results: </jats:bold> E‐cadherin, CD44, keratins K5/6, K8, K13, K14, K18 and pan‐keratin immuno‐staining were all significantly lower in patients ‘out of season’ compared with normal controls. No structural differences in the epithelium were observed between the two groups. The epithelium of patients ‘in season’ was thicker and immuno‐staining of the above markers similar to controls.</jats:p><jats:p><jats:bold>Conclusions: </jats:bold> The expression of a wide spectrum of epithelial cell adhesion proteins and cytoskeletal elements is downregulated in the conjunctiva of SAC patients ‘out of season’ compared with normal controls. We suggest that this could have an important impact on the ability of the epithelium to protect itself against allergen penetration, potentially influencing the development and course of allergic eye disease and offering a novel area for therapeutic control.</jats:p>