The rate of physeal growth slows as an animal matures with changes in mRNA gene expression due to the altered cellular activity. To measure the change in gene expression during the juvenile growth period, the femoral head, enclosing the proximal femoral physis, primary spongiosa, and articular cartilage, was collected from both femora of 16 female Sprague-Dawley rats between 4 and 10 weeks of age. One femur of each rat had had a mid-diaphyseal femoral fracture at 4 weeks of age. RNA was extracted and hybridized to 16 Affymetrix Rat Genomic 230 2.0 GeneChip microarrays with probe sets for 31,000 genes of which 18,200 were expressed. Of these, 8002 genes had a significant change in gene expression during growth, about half increasing and half decreasing. These changes included up-regulation with time of genes related to cartilage, blood vessels, osteoprotegerin, osteomodulin, and most ribosomal proteins. There was down-regulation with maturity of genes related to bone, growth-promoting cytokines, G proteins, GTPase-mediated signal transduction factors, cytokine receptors, mitosis, integrin-linked kinase, and the cytoskeleton. In summary, the slowing of growth with maturity was associated with changes in mRNA gene expression in the femoral head for a large number of genes. These changes in gene expression between young and mature rats suggest factors which are important for the support of the rapid linear growth during early life.