Cerebral white matter damages can be detected and characterized using magnetization transfer (MT) imaging. In this study a fully automated method of measuring and analyzing the MT of the whole human brain is presented and assessed. A 3D-FLASH sequence with off-resonance RF pulse was optimized for fast, volumetric MT measurements. The postprocessing software developed for this purpose includes a SPM99-based segmentation algorithm, a visualization tool, and a histogram-based MT parameter analysis. The reproducibility of the method was tested with phantom measures and in studies on nine healthy volunteers. Small variances (0-1.6%) and therefore, a high reproducibility of MT parameter measurements were found in vitro, slightly higher variances in volunteer investigations (0.7-4.0%). With our technique, we expect to be able to better recognize and follow up the progression of white matter diseases. Due to the high reproducibility, this volumetric approach is specifically suitable for longitudinal MT studies.