During the early stages of articular osteochondrosis, cartilage is retained in subchondral bone, but the pathophysiology of this condition of growing humans and domestic animals is poorly understood. A subtractive hybridization study was undertaken to compare gene expression between the cartilage of early experimentally induced equine osteochondrosis lesions and control cartilage. Of the many putative differentially expressed genes identified, eight were confirmed by quantitative PCR analysis as differentially expressed, in addition to those already known to be associated with early lesions. Genes encoding vacuolar H þ -ATPase V 0 subunit d 2 (ATP6V0D2), cathepsin K, integrin-binding sialoprotein, integrin aV, low density lipoprotein receptor-related protein 4, lumican, osteopontin, and thymosin b4 (TMSB4) were expressed at higher levels in lesions than in control cartilage. These genes included 34 genes not previously identified in cartilage. Some genes identified as associated with early lesions are known chondrocyte hypertrophyassociated genes, and in transmission electron microscopy studies normal hypertrophic chondrocytes were observed in lesions. Differential expression of ATP6V0D2 and TMSB4 in the cartilage of early naturally occurring osteochondrosis lesions was confirmed by immunohistochemistry. These results identify novel osteochondrosis-associated genes and provide evidence that articular osteochondrosis does not necessarily result from failure of chondrocytes to undergo hypertrophy. Most bones grow through the process of endochondral ossification, in which chondrocytes play a central role. Growth cartilage is comprised of chondrocytes arranged in zones that correspond to the stages of an organized program of sequential biological events. A zone of resting chondrocytes blends into a zone of proliferative chondrocytes and then a zone of hypertrophic chondrocytes, which ultimately undergo physiological death. Within the zone of hypertrophy, the cartilage matrix surrounding individual chondrocytes is partially degraded, leaving behind cartilage remnants that form vertical struts onto which bone matrix is deposited by invading osteoblasts (reviewed by Mackie et al., 2011 1 ). The processes of chondrocyte proliferation, differentiation, and hypertrophy are tightly regulated by a variety of growth factors, hormones, transcription factors, and components of the cartilage matrix. Many of these factors have been characterized, but it is likely that more remain to be identified. The process of physiological death undergone by chondrocytes is less well characterized, and there has been a debate in the literature as to whether it occurs through apoptosis or a non-apoptotic mode of death.2,3 Moreover, the chondrocytes in growth cartilage express factors capable of regulating the behavior of cells in the invading ossification front, including vascular endothelial cells, osteoclasts, and osteoblasts.