Dedifferentiated chondrosarcoma (DDCS), a highly malignant variant of chondrosarcoma (CCS), is characterized by high-grade sarcoma adjacent to low-grade chondroid tumor. Owing to its complicated composition, the histogenesis of this tumor remains controversial. Earlier, we carried out DNA microarray analysis using chondrosarcomatous tissues, and found that Sox9 and runt-related transcription factor 2 (Runx2) were differentially expressed in CCS compared with DDCS. Here, we analyzed Sox9, Runx2, Col2a1, and Col1a1 in NDCS-1 (DDCS) and SW1353 (CCS) cell lines using reverse transcriptase-polymerase chain reaction, western blot, and immunocytochemistry. The results showed high expression of Runx2 and Col1a1, and low expression of Sox9 and Col2a1 in NDCS-1 cells. In SW1353 cells, however, gene expressions were reversed. These findings provide evidence that Sox9 and Runx2 are involved in the occurrence and development of DDCS.