Magnetic resonance (MR) imaging is the principal imaging technique for the diagnosis of multiple sclerosis (MS). However, quantifying the number and extent of lesions on MR images manually is arduous. The authors have developed a computerized three-dimensional (3D) quantitative system to assist in the identification and analysis of MS lesions in proton-density (PD)- and T2-weighted volumes of the head. The system provides intuitive, interactive operations that allow flexible extraction of information from the data. Use of the system to analyze MR examinations of a phantom containing regular "lesions" showed that accurate (average error, < 0.21 cm3) and precise (10% or better for lesions > 1 cm3) measurements of objects less than 7 cm3 is possible, and that an estimate of the quantization error predicted the uncertainty in the volume. Analysis of four MR examinations of a chronic-progressive MS patient conducted over an 18-month period was performed. A two-dimensional histogram showing the frequency of voxels with particular PD- and T2-weighted intensities revealed a distinct cluster only in histograms of sections that contained lesions. Measurements and 3D volume rendering of lesions clearly showed changes in lesion shape, position, and size.