A semiautomated computerized method of in vivo morphometric analysis that is based upon high-resolution three-dimensional magnetic resonance imaging has been developed. This morphometric method is efficient and is of greater analytical precision than any other morphometric method currently applied to living human tissue. Including error inherent in image data acquisition, the aggregate error of the methodology, as estimated by the phantom studies, ranges from 4.5 to 9.6%, with incremental error above 4.5% a function of magnetic resonance slice thickness. This method was applied to magnetic resonance scans of 7 normal volunteers. The derived volumes of whole brain and of individual substructures were closely concordant with previously published volumes of normal fresh (unfixed) brains obtained post mortem. This morphometric methodology is potentially applicable to any structure or lesion that can be visualized by magnetic resonance imaging.