Morphometric analysis of brain structures recently has become a main focus of interest in studies of some neuropsychiatric diseases. Limitations in imaging and mensuration methodology that is available currently for quantitative measurement of anatomic structures have prompted the development of a computerized system to study brain morphometry. A menudriven semi-automated computer system has been developed to assess in vivo brain morphometry using three-dimensional (3-D) magnetic resonance (MR), gradient echo, contiguous images of the whole brain. Accuracy of the system was tested with phantoms creating white on black contrast to simulate the brain tissue surrounded by subarachnoid cerebrospinal fluid (CSF), and a second set of phantoms creating black on white contrast to simulate the ventricular system in the brain tissue. The first set of phantoms was composed of three water-filled balloons (spherical, elliptical, and multiform) and a fresh postmortem brain. The second set of phantoms consisted of three rods of different diameters from a simple geometric plexiglass rod phantom and a life size cast of a human ventricular phantom. System accuracy was generally within 2.0% of the true volumes. System reliability was evaluated in three patient populations; 12 patients with Alzheimer's disease, nine with schizophrenia and nine healthy controls age-matched to the patients with Alzheimer's disease. Two independent observers measured the ventricular systems of these patients. Reliability of the system was addressed by the correlation between the two sets of measurements. For the sample as a whole, and each of the subgroups, the correlation between the two observers was 0.99. This system compares favorably with other morphometric methods reported.