Arterial hypertension is one of the most significant medical and social problems, being widespread and associated with the risk of renal failure, cardiovascular and cerebrovascular complications. The aim was to investigate the morphofunctional state of microglia in different regions of the rat brain in the setting of arterial hypertension. Brain samples from spontaneously hypertensive SHR rats aged 3–8 months (n = 4) were used as study material. Normotensive WKY rats of the same age (n = 3) were used as the control group. The work was performed using immunohistochemical analysis and confocal laser microscopy. During the quantitative analysis, we were seeking to determine the number of microgliocyte bodies and the area occupied by the bodies and processes of these cells per 1 mm² of the nervous tissue. An immunohistochemical reaction for calcium-binding protein Iba1 revealed that in rats with arterial hypertension, microglia in the cerebral cortex, striatum, subcortical white matter and subfornical organ showed morphological signs of activation: increased body size and thickening of the processes of these cells. The strongest activation is demonstrated by microglia of the subfornical organ, which is in a preactivated state in normotensive rats. The performed statistical analysis revealed a trend towards an increase in the amount of microglia in the brain in SHR rats compared to animals in the control group. The Iba1/CD68 double immunofluorescence reaction showed no changes in the amount and/or distribution of lysosomal CD68 protein in spontaneously hypertensive rats compared to control group. The results obtained indicate chronic activation of microglia in the brain of spontaneously hypertensive rats. Activation of microglia in this case is not accompanied by an increase in the phagocytic activity of these cells.