The aim of the study was to evaluate the microsphere technique for the quantitative assessment of regional cerebral blood flow (rCBF) at different time points in the same animal. Yellow-green and red fluorescent microspheres with a diameter of 15 microm were injected into the rat at two different time points via a cannula inserted into the left ventricle of the heart. The reproducibility of the rCBF measurements in normocapnic conditions (n=7) and the responsiveness of the flow to hypercapnia induced by 7% CO(2) (n=7) was examined. The fluorescent spheres were counted on 100 microm vibratome sections of perfusion-fixed brains and rCBF was calculated. The median total CBF in normocapnic rats was 224 ml/min/100 g for the first microsphere injection and 216 ml/min/100 g for the second one. In the hypercapnic group CBF amounted to 400 ml/min/100 g and after 30 min of normocapnia decreased to 178 ml/min/100 g. No differences between the left and right hemisphere were found and there was no indication that the first injection might have influenced the second one. The described approach allows combining the assessment of rCBF at different time points in physiological or pathological conditions with histological evaluation of related morphological alterations in the same brain region of the same animal.