We identified changes in proapoptotic and extracellular matrix-related gene expression with prolonged storage of fresh osteochondral allografts using gene array analysis to better understand the process of graft degradation during storage. Six human distal femurs were obtained according to standard organ harvesting protocol and stored in serum-free allograft media. Each was examined at baseline (within 72 hours postmortem), 21 days (average time of implantation), and 35 days (maximum time to implantation) for proapoptotic and extracellular matrix-related gene expression using two 100-gene microarrays, cell viability using confocal microscopy, and proteoglycan synthesis via SO4 incorporation. We found numerous genes showing upregulation associated with increased storage time, including CD30, CD30 ligand, Fas, Fas ligand, tumor necrosis factor-alpha, and several caspases. Cell viability and proteoglycan synthesis also were significantly decreased with increased storage. Loss of chondrocytes via apoptosis is likely a key determinant of osteochondral allograft viability during storage, whereas extracellular matrix degeneration may occur at a later stage. These findings provide targets for future media modulation. Improved graft viability and the potential for lengthened storage periods through improved storage conditions may improve clinical outcomes and availability of fresh osteochondral allografts.