This study investigated the cytokine expression profile in alkali-burned mouse corneas, in order to elucidate the mechanisms of corneal damage and repair. The cytokines expressed in alkali-burned corneas were identified by polymerase chain reaction (RT-PCR), then quantitated using ELISA. Based on the ELISA results, immunohistochemical analyses were performed to localize cytokine expression. Among the ten cytokines examined, IL-1 (IL-1 beta), IL-6, IL-10 and TNF-alpha mRNA were expressed in alkali-burned corneas. Quantitation revealed that IL-alpha and IL-6 were strongly induced in the early stages of alkali burn, peak production of IL-1 alpha (53.2 pg/cornea) and IL-6 (23.6 pg/cornea) occurring at days 3 and 7, respectively. The production of IL-10 and TNF-alpha was not significantly elevated during the 42 day period after burn. Immunohistochemical analyses revealed that both IL-1 alpha and IL-6 were mainly localized in regenerating epithelial basal cells. IL-1 alpha and IL-6 levels in the cornea are dramatically elevated in the regenerated epithelium during the early stages of alkali burn, and may play an important role in associated corneal damage and repair.