Conventional MRI studies have not provided definitive evidence of progressive loss of brain volume in the early stages of schizophrenia, although more subtle changes may have gone undetected. We have looked for such subtle changes using volumetric MRI and magnetization transfer imaging (MTI), an advanced MRI technique sensitive to subtle neuropathological abnormalities. Magnetization transfer images and high-resolution volumetric T1-weighted images were acquired from 16 patients with first-episode schizophrenia at the start of the study and 3.7 years later. A group of 12 healthy controls were also scanned on two occasions. Images were processed using a voxel-based approach that allows whole-brain analysis. There was a group difference with a significant volume loss in the patients' white matter adjacent to the lateral ventricles in the right and left temporal lobes, in medial temporal gyrus, and in the white matter in and around the right middle frontal gyrus. No cortical differences were detected between the groups using MTI or volumetric MRI. The absence of any time-by-group interaction suggests that these abnormalities do not progress in the early stages of the disease. The results of the study need to be interpreted in the light of the small sample size and of the limitations of current image analysis methods.