OBJECTIVE To investigate the differential expression of immediate-early genes c-jun and c-fos in primary visual cortex of rat early after acute optic nerve injury and the relationship between immediate-early gene expression and injury degree of optic nerve. METHODS This was an factorial design of two factors. 55 male Sprague-Dawley rats were divided into groups randomized. Unilateral optic nerve crush injury or transection was performed in rats to obtain acute partial or complete monocular optic nerve injury models. Frozen sections through visual cortex were cut in normal rats and model rats respectively at 2 h, 1 d, 3 d, 1 week and 1 month after operation. Expression of c-Jun and c-Fos was detected in primary visual cortex by means of immunohistochemistry. Statistical comparisons were made using variance analysis of factorial design. RESULTS Statistically significant different of c-Jun expression existed between optc nerve crash injury and transection models (F = 50.344, P = 0.000). Increased expression of c-Jun in primary visual cortex could be observed at 2 h postoperation, and reached peak value at 1d postoperation. The extent of increased c-Jun expression was much higher in optic nerve transection models than crush injury models. Statistically significant different of c-Fos expression existed between optc nerve crash injury and transection models (F = 62.232, P = 0.000) Decreased expression of c-Fos in primary visual cortex could be observed at 2 h postoperation in optic nerve crush injury models, and reached bottom at 3 d postoperation. The extent of decrease of c-Fos expression was lower in optic nerve transection models than crush injury models and transient increased expression could be observed at 2 h postoperation. CONCLUSIONS The expression of immediate-early genes c-Jun and c-Fos changed shortly after optic nerve injury. They may act in opposite direction in the primary visual cortex.