We examined gene expression profiles in rat adrenal glands using genome-wide microarray technology. Gene expression levels were determined in four rat strains, including one normotensive strain [Wistar-Kyoto (WKY)] and three substrains derived from WKY rats: spontaneously hypertensive rats (SHR), stroke-prone SHR (SHRSP) and malignant SHRSP (M-SHRSP). This study represents the first attempt at using microarrays to compare gene expression profiles in SHR, SHRSP and M-SHRSP adrenal glands, employing WKY as controls. Expression measurements were made in these four rat strains at 6 and 9 weeks of age; 6 weeks of age covers the pre-hypertensive period in SHR and SHRSP, and 9 weeks of age is the period of rapidly rising blood pressure (BP). Since the aim of this study was to identify candidate genes involved in the genesis of hypertension in the SHR substrains, we identified genes that were consistently different in their expression, isolating 87 up-regulated genes showing a more than 4-fold increase and 128 down-regulated genes showing a less than 1/4-fold decrease in at least two different experiments. We classified all these up- or down-regulated genes by their expression profiles, and searched for candidate genes. At 6 weeks of age, several BP-regulating genes including sparc/osteonectin (Spock2), kynureninase (Kynu), regulator of G-protein signaling 2 (Rgs2) and gap junction protein α1 (Gja1) were identified as up-regulated, and urotensin 2 (Uts2), cytoplasmic epoxide hydrolase 2 (Ephx2), apelin (Apln), insulin-like growth factor 1 receptor (Igf1r) and angiotensin II receptor-associated protein (Agtrap) were identified as down-regulated. The Kynu and Ephx2 genes have previously been reported by other groups to be responsible for hypertension in SHR; however, our present approach identified at least seven new candidate genes.