Mandibular condylar cartilage can be distinguished from articular and growth cartilages of long bones based on several differences in morphology, physiology, and function between these structures. However, there is almost no information available on the types of genes that contribute to these differences. In this study, genes that were differentially expressed in mandibular condylar and growth cartilages in 1-week-old rats were investigated using fluorescent differential display (FDD) and laser microdissection (LMD). A number of genes were identified by FDD including chondromodulin-1 (ChM-1), which is known to be an angiogenesis inhibitor of endochondral ossification. ChM-1 expression was then compared with that of tenomodulin (TeM) in mandibular condylar and tibial cartilages of 1- and 5-week-old rats using real time PCR (RT-PCR), immunohistochemistry, and in situ hybridization. There was negligible detection of ChM-1 mRNA and protein in mandibular condylar cartilages compared to tibial cartilages of 1- and 5-week-old rats. On the other hand, TeM mRNA was more abundant in mandibular condylar cartilage than in tibial. These observations demonstrated that gene expression in mandibular condylar cartilage differed from other types of cartilage such as articular and growth ones.