Disturbed gene expression may disrupt the normal process of repair and lead to pathologic situations resulting in excessive scarring. To prevent and treat impaired healing it is necessary to first define baseline gene expression during normal repair. The objective of this study was to compare gene expression in normal intact skin (IS) and wound biopsies (WM), using suppression subtractive hybridization (SSH) to identify genes differentially expressed during wound repair in horses. Tissue samples included both normal intact skin and biopsies from 7 day old wounds. IS cDNAs were subtracted from WM cDNAs to establish a subtracted (WM-IS) cDNA library. 226 non-redundant cDNAs were identified. Detection of genes previously shown to be expressed 7 days following trauma, including COL1A2, ANXA2, COL6A3, ACTB, FGF-7, LAMR1, MMP1, SPARC and TIMP-2, supported the validity of the experimental design. An RTPCR assay confirmed an increase or induction of the cDNAs of specific genes (COL1A2, MMP1, DSPG2, CD68, CD163 and ADAM9) within wound biopsies. Among these, COL1A2 and MMP1 had previously been documented in horses. 68.8% of the cDNAs had not previously been attributed a role during wound repair, of which SSAT, SERPINB10 and SNX9 were highly expressed and whose known functions in other processes made them potential candidates in regulating the proliferative response to wounding. In conclusion, we have identified novel genes that are differentially expressed in equine wound biopsies and which may modulate repair. Future experiments must correlate changes in mRNA levels for precise molecules with spatio-temporal protein expression within tissues.