In this study, we describe and adapt the relevant methods of magnetic resonance (MR) and stereology to estimate total brain volume (TBV), cerebral and cerebellar volume and their volume fractions within the brain. The study included 15 (8 males, 7 females) controls and 15 (8 males, 7 females) patients with Alzheimer's disease. The patients' MR images were obtained in both sagittal and axial planes. The volume and volume fraction of the total brain, cerebrum and cerebellum were determined on MR images using the point-counting approach of stereological methods. The volume fractions of the cerebrum to TBV and cerebellum to TBV in the control group were 66.38% and 67.87% in axial and sagittal planes, and 12.05% and 12.81% in axial and sagittal planes, respectively. The volume fractions of the cerebrum to TBV and cerebellum to TBV in the Alzheimer group were 52.40% and 56.26% in axial and sagittal planes, and 10.00% and 10.38% in axial and sagittal planes, respectively. The Alzheimer subjects showed significantly lower cerebral and cerebellar volume fraction to TBV than the control subjects (p<0.001). No significant difference was found in either group with regard to gender or planes (p>0.05). The present evaluation of TBV, cerebral and cerebellar volume and volume fractions can be done on any complete set of MR imaging, in which the plane scan distance and magnification factor are known, as they are in MRI. In conclusion, the cerebral and cerebellar to TBV volume fractions can be important tools in determining brain atrophy and can be estimated by the stereological method.