Although the growth plate matrix area fraction increases after irradiation, extracellular matrix (ECM) gene expression in this context has not been studied. The hypothesis was that normally expressed ECM genes would be upregulated after irradiation. The right limbs of six Sprague-Dawley 5-week-old rats were irradiated with the left limbs as controls. Half of the animals were harvested after 1 week and half after 2. Microarray was conducted from normal and irradiated tibial growth plate proliferative zone (PZ) and hypertrophic zone (HZ) chondrocytes separated by laser microdissection at each time point. In situ hybridization (ISH) and real-time polymerase chain reaction (PCR) were used to confirm expression of selected genes. At 1 and 2 weeks after irradiation, both normally expressed ECM genes and others not highly expressed in the normal growth plate showed upregulation. Metalloproteinases and cathepsins were downregulated. PZ gene expression after irradiation exhibited features of the normal HZ, suggesting premature terminal differentiation. ECM genes not highly expressed in the normal growth plate included several members of the small leucine-rich proteins and the ezrin–radixin–moesin family. The effects of irradiation on cathepsin K (Ctsk), integrin binding sialoprotein (Ibsp), and procollagen II alpha 1 (Col2a1), as determined by ISH and real-time PCR, were highly correlated with the microarray results. Accumulation of matrix following radiation injury to the growth plate correlated well with changes in gene expression. Upregulation of genes not normally highly expressed in the noninjured growth plate suggests their importance in the injury and repair response.