Distinguishing chondrosarcoma from chondroblastic osteosarcoma can be difficult and highly subjective, especially on a small biopsy specimen. This distinction is critical in determining the most accurate prognosis and appropriate treatment modality, as adjuvant chemotherapy with surgery is standard treatment for osteosarcoma, whereas chondrosarcoma is generally treated by surgical excision alone. Cartilaginous neoplasms have recently been shown to frequently (56%) harbor gene mutations in the metabolic enzymes isocitrate dehydrogenase 1 (IDH1) and IDH2 (IDH1>IDH2), whereas other mesenchymal tumors lack these genetic aberrations. We investigated whether the presence of IDH1/2 mutations can be used to distinguish chondrosarcoma from chondroblastic osteosarcoma. Tumors including 25 predominantly high-grade chondrosarcomas and 65 osteosarcomas (44 chondroblastic osteosarcomas and 21 mixed osteosarcomas with a chondroblastic component) were evaluated, and a total of 59 cases (66%) were suitable for genotyping. Mutational analysis was performed using a multiplexed polymerase chain reaction genotyping platform to query for hotspot mutations in the genes IDH1 at codon R132. IDH1-negative cases underwent Sanger sequencing of IDH2 exon 4. No osteosarcomas (0/36) and 61% of chondrosarcomas (14/23) harbored a somatic mutation in IDH1/2, with the majority (86%) of mutations found in the IDH1 gene. IDH1/2 mutation analysis appears to be a promising biomarker for the distinction of chondrosarcoma from chondroblastic osteosarcoma. A positive result strongly favors the diagnosis of chondrosarcoma over chondroblastic osteosarcoma. The presence of IDH1/2 mutations can also help confirm the diagnosis of dedifferentiated chondrosarcoma when the tumor displays osteosarcomatous differentiation.