Compared to Wistar-Kyoto (WKY) normotensive control rats, spontaneously hypertensive (SHR) rats have significantly reduced brain weights (-10.6%) and brain volumes (-11.8%). Computerized morphometric analysis of soma cross-sectional areas of single neurons in 12 selected hypothalamic regions revealed significant differences between SHR and WKY animals. Neurons from the periventricular, medial and lateral preoptic nuclei and ventromedial hypothalamus show significantly increased soma cross-sectional areas in SHR animals when compared to normotensive controls. Cells located in the two circumventricular organs, organ vasculosum lamina terminalis (OVLT) and subfornical organ (SFO), also showed significantly greater cross-sectional areas in the SHR. In contrast, neurons in the paraventricular and arcuate nuclei and dorsomedial hypothalamus were significantly smaller in spontaneously hypertensive rats when compared to normotensive controls. Only neurons in supraoptic nucleus, lateral and anterior hypothalamus have equivalent cross-sectional areas in WKY and SHR animals. Differences also exist in the number of cells in certain nuclei in SHR animals. Cell densities in periventricular preoptic nucleus, paraventricular nucleus, arcuate nucleus, ventromedial and anterior hypothalamus, organ vasculosum lamina terminalis and subfornical organ were reduced in SHR animals compared to WKY controls. Because of decreased brain weight and volume along with observed morphometric differences in individual neuronal soma size and cell densities, it is suggested that the SHR brain differs significantly from normotensive control rats. The differences may underlie some of the abnormalities in cardiovascular and endocrine regulation associated with neurogenic hypertension.