Low-grade intramedullary cartilage tumors include enchondroma and grade 1 chondrosarcoma. Classification based on radiopathologic correlation guides treatment, typically observation for asymptomatic enchondroma and surgery for chondrosarcoma. However, some tumors elude classification because radiographic and morphologic findings are equivocal. To date, no ancillary tests are available to aid the diagnosis of such indeterminate or suspicious tumors. We investigated the genomic landscape of low-grade cartilage tumors to determine the profile. We studied 10 each enchondroma, grade 1 chondrosarcoma, and suspicious cartilage neoplasms, respectively, by capture-based next-generation sequencing targeting 479 cancer genes and copy number. In enchondroma, IDH1 or IDH2 hotspot activating mutations and/or COL2A1 alterations were identified in 70% and 60% of cases, respectively; copy number changes were rare (20%). Suspicious cartilage neoplasms had frequent hotspot mutations in IDH1 or IDH2 and alterations in COL2A1 (90% and 70%, respectively); copy number changes were rare (20%). Overall, 80% of suspicious cartilage neoplasms were genomically indistinguishable from enchondroma. In contrast, 20% of chondrosarcoma had IDH1 or IDH2 alterations, 100% demonstrated alteration of COL2A1, and 70% had genomes with numerous copy number gains and losses. In total, 80% of chondrosarcomas demonstrated additional pathogenic mutations, deep deletions, or focal amplifications in cancer genes, predominantly CDKN2A. These results demonstrate distinct genomic profiles of enchondroma and grade 1 chondrosarcoma. Further, sequencing may aid in the correct classification of diagnostically challenging tumors. Additional pathogenic alterations (such as in CDKN2A) or numerous copy number gains or losses would support a diagnosis of chondrosarcoma although the absence of such findings does not exclude the diagnosis.