The rate of bone formation to bridge a fracture gap slows with age. To explore potential pathogenic mechanisms and possible negative-feedback responses by the skeleton to this reduced rate of healing, mRNA transcripts up-regulated more and/or longer were studied in older rats with delayed healing. Female rats at 6 (young), 26 (adult), and 52 (old) weeks of age received unilateral diaphyseal femoral fractures with intramedullary rod stabilization. At 0, 0.4, 1, 2, 4, and 6 weeks after fracture, the fracture site was harvested. Total RNA was extracted, cRNA was prepared, and the cRNA was hybridized to 54 Affymetrix U34A microarrays (three arrays/age/time point). Transcripts for 180 genes were identified as up-regulated more and/or longer in old rats with delayed fracture healing. Of these, 60 were selected for more intense review. Significantly more and/or longer expression was seen in genes related to myofibroblasts, cell proliferation, calcification inhibition, TGF-beta activity, lipid metabolism, cell adhesion, and the cytoskeleton. Further study is needed to determine if these up-regulated transcripts are related to the pathological processes which slow healing or are related to attempts by the fracture tissue to stimulate bone to bridge the fracture gap.