Fukuyama-type congenital muscular dystrophy (FCMD), the second most common childhood muscular dystrophy in Japan, is characterized by the association with severe brain anomalies such as pachygyria and focal interhemispheric fusion. Conventional imaging techniques such as X-ray CT scan and MRI are ineffective for visualization of these brain surface anomalies. Here we investigated the efficacy of three-dimensional (3-D) reconstruction of brain surface MR images for the detection of brain anomalies in FCMD patients. 3-D brain surface MR images clearly visualized anomalies of cerebral gyrus such as pachygyria, as well as focal interhemispheric fusion. In addition, reconstructed horizontal images visualized structural derangement such as abnormal protrusion of white matter into gray matter. MR image abnormalities were confirmed by autopsy in 1 patient. These abnormalities were never observed in Duchenne muscular dystrophy (DMD) patients. Our results indicate the efficacy of the present method for the differential diagnosis between FCMD and DMD with severe mental retardation, which is essential for the genetic study to identify the causative gene of FCMD.