Hereditary multiple exostoses (HME) is an autosomal dominantly inherited disorder characterized by multiple benign cartilage-capped exostoses. Clinical manifestation of the disease is heterogenous. Overriding toes, scoliosis, spinal cord compression, and brachydactyly caused by shortening of metatarsals are rare findings. EXT1 and EXT2 are the genes responsible in most HME patients. We have characterized 11 HME families and 6 sporadic cases involving a total of 37 patients and performed mutational analysis of EXT1 and EXT2. Structural modeling of the wild and mutant proteins was also performed. Thirteen mutations were identified, including 8 that are novel. Among the novel mutations in EXT1, c.1004T>G-associated HME exhibited overriding toes and scoliosis, c.1883+2T>A-associated HME exhibited brachydactyly, and c.459_460delCT-associated exostosis arising from vertebra T4 caused spinal cord compression. Our structural predictions revealed four domains in the proteins encoded by EXT1 and EXT2: signalP, transmembrane regions, exostosin, and glyco_transf-64. The mutations truncated either part or whole of the exostosin domain and/or the C terminus of the glyco_transf-64 domain, or occurred within one of the domains. Our results provide new data for genetic diagnosis, identification of presymptomatic carriers, phenotype-genotype correlation, and understanding of the mechanisms of disease.