A number of researches have studied the neurophysiological bases of amblyopia, and most of these studies focused on the gray matter alterations. For the purpose of elucidating whether there would be any changes in the white matter, a combination of high-resolution anatomic MRI and vision tests were used to compare a group of children with ametropic amblyopia and control subjects. An automated and unbiased method called voxel-based morphometry (VBM) was employed to analyze the anatomical brain images. After performing two sample t-tests, decreased white matter volume were detected in ametropic amblyopic children versus controls. The involved regions were predominantly in the occipital lobes bilaterally, and a smaller region in middle frontal lobe. It indicates that visual defects in amblyopia can influence the development of white matter.