Previous studies have shown that regional variation in ion channel gene expression contributes to electrical heterogeneity within the walls of the cardiac ventricles. To map the extent of regional variation in gene expression in the ventricular walls and to begin to understand its genesis we have performed a microarray analysis of gene expression in the epicardial and endocardial tissues of the rat adult left ventricle. While the vast majority of the genes are expressed at uniform levels across the ventricular wall, a total of 36 transcripts (representing less than 0.1% of the genes expressed in the ventricle) are expressed more abundantly in either epicardium or endocardium. One of these differentially expressed genes is the sodium channel gene Scn5a, which is expressed at higher levels in the endocardium than in the epicardium of rat heart. The transcription factor genes Irx3, Irx5 and Etv1 were found to be expressed in transmural gradients across the ventricular wall of rat heart and also of canine heart. The Irx3 and Irx5 genes were expressed in an inverse pattern to that of the Kcnd2 (Kv4.2) gene in rat heart, suggesting that these transcription factors may act as negative regulators of Kcnd2 expression in vivo.