Spondyloepiphyseal dysplasia tarda (SEDT) is an X-linked skeletal dysplasia. Patients show disproportionate short stature with short trunk and barrel-shaped chest, which usually become pronounced in late childhood. The radiologic findings are characterized by narrow intervertebral disc spaces and moderate epiphyseal dysplasia of long bones. Here we report a case of SEDT with a novel frameshift mutation in TRAPPC2, the disease-causing gene of SEDT. This is the first Korean report with SEDT confirmed by genetic testing.