Spontaneously hypertensive rats (SHR) are a well-known animal model for hypertension. We have previously identified eleven differentially expressed genes in the kidneys between SHR/Hos and Wistar-Kyoto rats (WKY/Hos) using an oligonucleotide microarray and analyzed the correlation between these genes and hypertension. In the present study, we analyzed the differentially expressed genes in the kidneys between SHR/NCrj and WKY/NCrj obtained from an other source to clarify the common and/or specific gene expression between the different sources. Furthermore, expression changes in the representative genes were characterized by Northern blot analysis using samples prepared from a third source, the Izm strain. The comparison revealed quite different changes in the differentially expressed genes among them. Sequence analysis of one of the differentially expressed genes, cytosolic epoxide hydrolase, revealed that two haplotypes could in part explain the expression level. Our study showed the complex nature of the genetic heterogeneity between SHR and WKY from different sources.