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The purpose of this study was to test the hypothesis that a different incidence of apoptosis occurs in the mesenteric arteries of the spontaneously hypertensive rat (SHR) compared with its normotensive control the Wistar-Kyoto rat (WKY) at 1–2 weeks of age.We examined the incidence of apoptotic cells in the blood vessel wall of muscular arteries from the SHR and WKY at 1–2 weeks of age using two techniques of apoptosis measurement, DNA laddering and 3′-OH end labelling. We also measured the volume of the blood vessel wall components and lumen sizes with the confocal microscope to determine whether a differential incidence of apoptosis occurred between the two rat strains.We used phenol/chloroform extraction to isolate genomic DNA and assess DNA fragmentation, with gel electrophoresis to determine DNA laddering, and 3′-OH end labelling, where the enzyme terminal deoxynucleotidyl transferase catalyses the addition of fluoresceinconjugated nucleotides to the cut ends of DNA, to detect in situ DNA fragmentation. The volume per unit length of the blood vessel structural components was measured by optical sectioning with the confocal microscope.We found that the SHR had a significantly decreased incidence of cellular apoptosis over WKY. This was true for both the electrophoretic method where SHR had significantly less fragmented DNA (molecular size < 600 bp) than WKY (P = 0.01), and for the microscopic method where SHR had fewer labelled cells in both the adventitia (P = 0.01) and the media (P = 0.0001) layers of large mesenteric arteries. The volumes of the adventitia, media and lumen in the large mesenteric arteries were similar between the two strains at this age.These findings suggest that a differential incidence of cellular apoptosis at the age of 1–2 weeks may be responsible for the larger media volume found in older SHR and thus contributes to the development of hypertension in these animals.