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<b>Purpose:</b> Pathogenesis of <i>Acanthamoeba</i> keratitis involves breakdown of epithelial barrier, stromal invasion by <i>Acanthamoeba,</i> loss of keratocytes, inflammatory response and finally stromal necrosis. The loss of keratocytes, believed to be due to the phagocytic activity of the parasite, occurs disproportionate to and independent of the parasite load, thereby suggesting additional modes of cell loss. To test our hypothesis that the loss of keratocytes in <i>Acanthamoeba</i> keratitis is due to apoptosis, we did both histology and histochemistry on the corneal tissues. <b>Methods:</b> Routine Haematoxylin and Eosin, Gomori&#x2032;s Methenamine Silver and Periodic acid Schiff stained sections of five corneal tissues from penetrating keratoplasty and eviscerated eyes were reviewed. TUNEL staining was done for morphological detection of apoptosis in three cases, using formalin-fixed, paraffin-processed tissues. <b>Results:</b> Histological changes were epithelial ulceration, loss of keratocytes in all layers, inflammation in anterior two-thirds of the stroma with necrosis, and deeper quiet stroma. <i>Acanthamoeba</i> trophozoites were found in the anterior stroma while the cysts were more in the deeper stroma, with minimal or no inflammatory response. TUNEL staining was positive in keratocytic nuclei in all layers. <b>Conclusions:</b> This study demonstrates that one of the modes of keratocyte loss in <i>Acanthamoeba</i> keratitis is by apoptosis, possibly in addition to the necrotic process and phagocytic activity of the parasite. The death of inflammatory cells also appears to be mediated by apoptosis.