Increased intraocular pressure is the main cause of glaucoma development. However, the systemic information of genes related to ocular hypertension has not yet been clarified. In the present study, oligomicroarray determined the profile of gene expression in the retina after ocular hypertension. A rat ocular hypertension model was constructed through photocoagulation by diode lasers. On postoperative days 7, 35, 60, 90, 180 and 360, the intraocular pressure and the gene expression profile were determined using an ophthalmotonometer and an Oligochip containing 35,000 oligonucleotides, respectively. Oligochip reliability was verified by real-time PCR, and the Oligochip data were analyzed through functional distribution analysis. In our study, we found that the intraocular pressure was significantly increased in a time-dependent manner but returned to the normal level on postoperative day 360. We also found that 1,692 genes were differentially expressed, including 719 upregulated and 973 downregulated genes. The chi(2) value of gene clusters related to transport function is significantly higher than that of other gene clusters as determined through function distribution analysis, suggesting that this group of genes plays an important role in the repair process of the optical nerve. In conclusion, the gene expression pattern at different time points of ocular hypertension was determined, which may contribute to clarify the molecular mechanism of glaucoma and to establish better therapeutic strategies to treat glaucoma. Copyright (C) 2010 S. Karger AG, Basel