Regular bouts of physical activity may cause changes in gene expression that accumulate over time and ultimately affect phenotypes, such as body weight, blood lipid profile, and tumor development. Furthermore, acute activity may affect gene expression and phenotypes differently depending on whether the individual is regularly inactive or active. One-month old male Sprague-Dawley rats (n=72) were equally divided into SED (standard laboratory cage, n=24), PA (large activity box, n=24), and EX (exercise wheel inside standard cage, n=24) groups. At three months of age, half the animals from each group were sacrificed at rest and the other half following 30 minutes of physical activity. RNA was extracted from cardiac tissue, and microarray analysis was performed on 27,000 genes. Select gene results were validated using qPCR. No gene expression differences occurred when comparing all 3-month old groups at rest. A relatively small percentage of genes (1.9%) were differentially expressed (p<0.05) following acute swim activity in all groups but only 37 unique and identifiable genes reached or exceeded two fold differences in expression. The genes Atf3, Fos, Apold1, and Pxdn were expressed differently among SED, PA and EX following acute activity, with a clear separation of the magnitude in gene expression with SED > PA > EX. Differences in gene expression levels in young physically inactive and active animals following acute activity have different regulatory roles in gene networks that affect health-related phenotypes.