Recently, an increasing number of volumetric studies of the human brain have been reported, using three-dimensional magnetic resonance imaging (3D-MRI). To our knowledge, however, there are few investigations on the relation of the volume and shape of voxels which constitute an MR image to the accuracy in volume measurement of an imaged object. The purpose of this study was to evaluate the effect of a different shape of voxel, that is, isotropic or anisotropic, as well as the volume of a voxel on the volume measurement based on the original image data and multiplanar reconstruction (MPR) data, respectively. In the experiment, we repeatedly acquired contiguous sagittal images of a single globe phantom with a known volume under the condition in which the volume and shape of voxels varied, on a 1.5T MR scanner. We used a gradient echo sequence (3D FLASH). The volume of the globe phantom from both original images and MPR ones was measured on workstations employing a semi-automated local thresholding technique. As a result, the smaller volume of voxels tended to give us the more correct measurement, and an isotropic voxel reduced measurement errors as compared to an anisotropic one. Therefore, it is concluded that the setting of voxel with both an isotropic shape and small volume, e.g., a voxel of 1 mm x 1 mm x 1 mm at present, is recommended in order to get a precise volume measurement using 3D-MRI.