Exercise training causes some physiological cardiovascular adaptations, which act to enhance cardiac and vascular functions at rest and during exercise. However, the molecular mechanisms of these adaptations are unclear. We investigated gene expression profiles of exercise training-induced cardiovascular adaptations. In the experiment, rats exercised on a treadmill for 4 or 8 weeks (4WT and 8WT). The differences in expression levels of 3,800 genes in the heart and abdominal aorta of sedentary control and exercise-trained rats were compared by the microarray analysis. Of the 3,800 genes analyzed in the microarray analyses, in the heart, a total of 45 genes (upregulation of 3 genes and downregulation of 42 genes) in the 4WT and 74 genes (upregulation of 50 genes and downregulation of 24 genes) in the 8WT displayed altered gene expression with exercise training. In the aorta, a total of 57 genes (upregulation of 35 genes and downregulation of 24 genes) in the 4WT and 31 genes (upregulation of 12 genes and downregulation of 19 genes) in the 8WT displayed altered gene expression with exercise training. Thus exercise training caused an alteration of many genes expression in the heart and aorta. The alteration of many genes expression in the heart observed in 8WT, whereas that in the aorta induced in 4WT. The observed difference in the change of the gene expression in the time course between the heart and aorta suggests that there may be a difference in the time course of exercise-induced physiological adaptation in the heart and aorta (e.g., formation of physiological cardiac hypertrophy and enhancement of arterial compliance).