Simpson-Golabi-Behmel syndrome (SGBS) is one of the overgrowth syndromes. Microdeletions of the glypican-3 (GPC3) gene were described by Pilia et al. (1996). Glypican-3 encodes a putative extracellular proteoglycan which is expressed in embryonic mesodermal tissues and plays an important role in embryonal growth. We report a Japanese patient with SGBS who had a single base deletion in the exon 7 of the GPC3 gene. This is the first report of a single base deletion of the GPC3 gene.