Homeobox genes encode a set of transcription factors of fundamental importance for body patterning during embryogenesis. Hoxa9-a13 and Hoxd9-d13 play an especially important part in vertebrate limb development. Synpolydactyly (SPD) is characterized by various malformations of the limbs. The expansion of the polyalanine tract in 1OXD13 is one of its major causes. Recently, there have been many analysis studies of HOXD13 in patients with SPD and limb malformations. We analyzed HOXD13 in 100 patients with limb malformations, which affects the limbs in the distal parts of the metacarpal and/or metatarsal bones. Seven mutations in the coding region and two mutations in the 5'-untranslated region were identified. All were novel mutations. In this study, the mutations were located upstream in the homeobox. Thus, translation of the homeobox was affected by upstream mutations. Consequently, this suggested the possibility that abnormalities in the hands and feet could be caused by novel HOXD13 gene mutations.