Aim To study the structural changes of basilar arteries during hypertension and the effects of captopril. Methods The animal model of stroke prone renovascular hypertensive rats might be divided into two groups, hypertension group and captopril treated group; one sham operated group was used asnormotensive control group. Each group took the observation of the structure of the basilar arteries under light microscope and transmission electrical microscope as well as analyses of morphometry at 4, 8, 12 weeks respectively. Results There were no obvious microscopic changes in basilar arteries of the hypertension group postoperation 4 weeks. The media thickness and wall to lumen ratio of the hypertension group were higher than those of captopril and sham operated groups (p<0.05). The intercellular spaces are broadened slightly at 4 weeks after operation; there were moderate ultrastructural damages at the end of 8 weeks, with the organelle oedema and partial lysis, interstitial dropsy; there were obvious ultrastructural damages at the end of 12 weeks, such as smooth muscle cell myofilament degeneration, fragmentation, lysis, and endoplasmic reticulumnecrosis dilataltion, mitochondria vacuolation, smooth muscle cell necrosis. The ultrastructure appearances of the captopril treated group were nearly normal. Conclusions Hypertension can cause hypertrophy and ultrastructural damage of basilar arteries. Captopril can prevent media hypertrophy of basilar arteries in experimental hypertensive rats and protect the ultrastructure against injury factors.