Cooling significantly affects cellular ultrastructure [1], as well as structural and functional state of histohematic barrier [2]. The aim of the given work was to study ultrastructural mechanisms of the permeability of brain cortex vascular endothelium under the effect of rhythmic hypothermia. Experiments were conducted on 180-220 g white males rats. Cooling of caudal part of animals was conducted in an automatic regimen by an ice water with 0.1 Hz frequency during 40 and 80 min. Experimental animals were narcotized by intraperitoneal injection of thiopenthal sodium and sodium hydroxybutyrate mixture in respect of 30mg/kg, 100 mg/kg of mass, correspondingly. Material from parietal lobe of brain cortex for electron-microscopic investigations was taken immediately after the effect finishing. Rectal temperature, which made 36-35C, was measured during the experiment. For electron microscopic investigations the samples were fixed by immerging into 4% glutar aldehyde on a phosphate buffer and were additionally fixed by 1% osmium fixative on a phosphate buffer. After dehydration in ethanol, samples were placed into the mixture of epoxy resins Epon-Araldit (Fluka, Sweden). Colloid carbon was used as a tracer for the estimation of permeability of brain capillary endothelium. with this aim 3-5 ml of 10% colloid carbon solution, prepared on 0,85% NaCl solution, were injected into a tail vein of the animals immediately after their decapitation. Preliminary estimation of the material quality was done on semi-fine tissue sections after the staining by toluidine blue.