The aim of this study was to characterize the molecular and histological changes that occur in the retina following central retinal artery occlusion (CRAO) in a mouse model. CRAO was induced in 60 mice by laser photoactivation of intravenously injected rose bengal. Mice were sacrificed at 3, 6, 12, and 24h and 7 and 21 days after CRAO induction for molecular analysis (5-13 mice/time point) and histological and apoptosis studies (3-4 mice/time point). Fundus examination and fluorescein angiography were also performed at various points. Retinal mRNA was analyzed for expression of T-cell antigen 1 (Thy-1), vascular endothelial growth factor (VEGF), heme oxygenase-1 (HO-1), and hypoxia-induced factor 1 alpha (HIF-1 alpha) using real-time polymerase chain reaction. The results showed that at 6-24h following CRAO induction, the retina was edematous, with interrupted blood perfusion. Fluorescein angiography showed reperfusion at 6h, and TdT-mediated dUTP nick end-labeling (TUNEL) assay revealed an increase in apoptotic cells in the first 24h. On histological sections, nuclear loss in the inner retinal layers was maximal on day 21. Thy-1 expression decreased to 30% of baseline (P<or=0.002). VEGF expression increased in the first 3h and gradually decreased thereafter, reaching 75% of baseline on day 21 (P<or=0.005). HO-1 was upregulated at all time points, with a peak at 12h. No change was noted in HIF-1 alpha expression at any time. In conclusion, CRAO in mice causes cell apoptosis in the inner layers of the retina, with a significant cell loss and a decrease in Thy-1 expression by 21 days. These changes are accompanied by a rise in expression of the ischemia-related protein HO-1 to a peak at 12h, with levels remaining above control values at day 21. Given the similarity of the mouse model to human CRAO, these findings may have implications for the future clinical management of CRAO.