Chordomas are rare malignant tumors arising in bone of the spheno-occiput, sacrum, and vertebral column which can cause neurological deficit. Current management of chordoma involves safe resection followed by radiation therapy. However, surgical resection is often subtotal and chordoma often recurs despite optimal therapy. Despite years of effort, effective adjuvant therapy for denovo, recurrent and metastatic chordoma are absent and 5-year survival is at best 65%. While no chemotherapeutic agent has been demonstrated to be effective against chordoma in vivo, a greater understanding of the genetics and molecular biology of chordoma is opening up avenues of investigation towards the rational development of targeted therapies. Although enthusiasm for the use of already established or new investigational agents will increase with greater understanding of chordoma biology, laboratory studies of these agents are important prior to incorporation into clinical human trials. The authors review the current state of knowledge regarding chordoma and offer insight into potential new therapies for this rare and challenging tumor.