Urotensin II (UII) and urotensin II-related peptide (URP) are novel vasoactive peptides that share urotensin II receptor (UT). We have recently reported that expressions of URP and UT were up-regulated in kidneys of rats with renal failure or hypertension. To clarify possible changes of the UII system expression in cardiovascular organs with hypertension, we examined the gene expression of UII, URP and UT in hearts and aortae of hypertensive rats. Furthermore, the expression was compared with that of endothelin-1 (ET-1). Quantitative reverse transcription polymerase chain reaction analysis showed that expression levels of UII mRNA and UT mRNA were significantly elevated in the atrium of 11–12-week-old spontaneously hypertensive rats (SHR) compared with age-matched Wistar–Kyoto rats (WKY). Moreover, UT mRNA expression was elevated in the ventricle of 11–12-week-old SHR. In the aorta, expression levels of URP mRNA and UT mRNA were significantly elevated in 11–12-week-old SHR compared with age-matched WKY, similarly to those in the kidney. In contrast, expression levels of ET-1 were significantly decreased in both the heart and the kidney of 11–12-week-old SHR compared with age-matched WKY. Immunohistochemistry showed that URP and UT were immunostained in cardiomyocytes, with weaker immunostaining in vascular endothelial and smooth muscle cells, in both SHR and WKY. These findings indicate that the gene expression of the UII system components (UII, URP and UT) and ET-1 is differently regulated in hypertension, and that the UII system in the heart and aortae may have certain pathophysiological roles in hypertension.