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Purpose Pterygium is an ocular surface disease associated with epithelial and fibrovascular outgrowth from the conjonctiva onto the cornea. Aquaporins are transmembrane water channels proteins implicated in cell migration and proliferation. This works aimed at analyzing the expression of AQP1, AQP3 and AQP5 in pterygia samples, compared to normal conjunctiva tissue. Methods Twenty five surgically removed pterygia were used for this study. Normal conjunctiva was obtained from7 human cadaveric donors. The expression of AQP1, AQP3 and AQP5 was measured by real‐time quantitative PCR (qRT‐PCR). The cellular distribution of those AQPs was assessed by immunohistochemistry. Results The expression of AQP1, AQP3 and AQP5 mRNAs was detected by qRT‐PCR in pterygia. In normal conjunctiva and pterygia, AQP1 was expressed on endothelial cells, myofibroblasts (but not on fibroblasts) and some inflammatory cells. AQP3 and AQP5 were expressed on epithelial cells and inflammatory cells. AQP5 was also expressed on fibroblasts and myofibroblasts. In pterygia, the epithelial expression of AQP3 and AQP5 was decreased at the leading edge of the lesion as compared to normal conjunctiva. AQP1 was strongly expressed in myofibroblasts in fibrotic lesions of pterygia. Conclusion AQP1, AQP3 and AQP5 are expressed in pterygia. Variation of AQP3/AQP5 epithelial expression and the strong induction of AQP1 expression in myofibroblasts suggest that those AQPs might be implicated in the pathogenesis of pterygium.