The past few years have seen an enormous increase in the knowledge of the signaling pathways and the transcription factors that control endochondral bone development. Recent studies of rare chondrodysplasias that exhibit disproportionate dwarfism due to the impairment of endochondral ossification have identified many responsible genes and have clarified pathogenic mechanisms of these diseases by using molecular genetics and biology. The details of human diseases related to collagen type II alpha1 (COL2A1), collagen type X alpha1 (COL10A1), parathyroid hormone (PTH) /parathyroid hormone-related protein (PTHrP) receptor, guanylate cyclase B (GC-B), sry-box 9 (SOX9), runt-related transcription factor 2 (RUNX2), which play important roles in the process of endochondral ossification, will be outlined.