This study was investigated that long term swimming exercises(period:4 and 8 weeks, frequency: 1h/5day/week) could modulate the expression of c-Fos, c-Jun and BDNF, analysed correlation between immediate-early gene and neurotrophic factor by swimming exercises in young and adult Sprague-Dawley rat brain. The results are followings: 1. The expressions of c-Fos protein following the swimming exercise for 4 weeks and 8 weeks were increased at 4 months elder rats and was more increased significantly in the post natal 4 weeks young rats. 2. The expressions of c-Jun protein following the swimming exercise for 4 weeks and 8 weeks were increased at the 4 months elder rat brain and was more increased significantly in the pst natal 4 weeks younger rat. 3. The expression of BDNF protein of the hippocampus was increased the all groups comparing to normal control group and the increased effects of swimming exercise was shown at the all 4 and 8 weeks exercise group. The results showed that the expression of immediate early genes, c-Fos and c-Jun was increased during the swimming exercises and the synthesis of BDNF enhanced in young and adult rat brains. It is suggested that the swimming exercises is not helpful tools for the memory and consciousness, but also enhance the regeneration of nervous system.