Cartilaginous lesions of bone are relatively common, and cover a large spectrum, from the benign enchondroma to the aggressive dedifferentiated chondrosarcoma. Differentiating between these lesions, particularly benign enchondroma and low-grade chondrosarcoma, can be quite challenging. This involves the assimilation and interpretation of clinical, radiographic, and histologic criteria. Molecular techniques to assist in distinguishing between the various subtypes are being developed, but have as yet not yielded any clinically significant contribution. Our lab, in conjunction with an international, cooperative chondrosarcoma clinical trial developed at HCI, uses cDNA microarray profiles to distinguish enchondroma from low-grade chondrosarcoma in an effort to better elucidate the diagnosis, prognosis, and eventual therapeutic interventions for cartilage cancer.