The purpose of the present study was to search for changes in gene expression patterns in the retina following optic nerve injury. We conducted a subtractive hybridization for comparison of the mRNAs in those retinas receiving optic nerve crush injury and those receiving sham operation. Both forward and reverse subtractions were carried out for 8-h and 24-h time points postoperatively. Resultant subtractive cDNA for each group was re-amplified and cloned to a plasmid. After DNA sequencing, the identity of subtractive cDNA was analyzed by blasting sequences to the Nonredundant gene database, Unigene database, and dbest database at NCBI. Thirty-four known genes and 32 EST were found in the forward subtractions. Forty-two known genes and 46 EST were found in reverse subtractions. Identities of the rest could not been found in the databases. To verify the subtractive results, RT-PCR was performed to test expression patterns of eight known genes found in the above analysis. Among these eight genes, seven demonstrated a statistically significant difference between the crushed eyes and the control eyes by quantitative image analysis. Together, our data show that expression of fatso, ephrin B2, NonO, Zfx, vitronectin, and XLRS increased after optic nerve injury, and expression of stathmin exhibited reduction after injury.