Osteochondrosis (OC) is a naturally occurring disease of the articular-epiphyseal cartilage and subchondral bone layers, leading to pain and decreased mobility. The objective of this study was to characterize gene and protein expression of apoptotic markers in chondrocytes surrounding cartilage canals and along the osteochondral junction of osteochondrosis (OC)-affected and normal cartilage, using naturally occurring disease in horses. Paraffin-embedded osteochondral samples (6 OC, 8 normal controls) and cDNA from chondrocytes captured with laser capture microdissection (4 OC, 6 normal controls) were obtained from the lateral trochlear ridge of femoropatellar joints in 14 immature horses (1-6 months of age). Equine-specific caspase-3, caspase-8, caspase-10, Fas, Bcl-2, BAG-1, TNFα, cytochrome , thymosin-β10, and 18S mRNA expression levels were evaluated by two-step real-time quantitative PCR. Percentage of cell death was determined using the TUNEL method. Protein expression of caspase-10, Fas, cytochrome , and thymosin-β10 was determined following immunohistochemistry. Statistical analysis was performed using the Wilcoxon rank sum test or two-sample -test ( < 0.05). In OC samples, there was significantly increased gene expression of caspase-10, Fas, cytochrome , and thymosin-β10 in chondrocytes along the osteochondral junction and increased Fas gene expression in chondrocytes adjacent to cartilage canals, compared to controls. In OC samples, higher matrix Fas and cytochrome protein expression, lower mitochondrial cytochrome protein expression, and a trend for higher cytoplasmic caspase-10 protein expression were found. Collectively, these results suggest that both extrinsic and intrinsic apoptotic pathways are activated in OC cartilage. Increased apoptosis of osteochondral junction chondrocytes may play a role in OC, based on increased gene expression of several pro-apoptotic markers in this location.