Background: The re-epithelialization process in equine wound healing is incompletely described. For epithelial cells to migrate during embryogenesis they undergo epithelial-to-mesenchymal transition (EMT); this phenotypic transition occurs during wound healing in humans and rodents, but it has not been investigated in horses. Hypothesis/objectives: To investigate keratinocyte differentiation and EMT in equine experimental excisional limb and body wounds healing by second intention. Animals: Six adult research horses. Methods and materials: Immunohistochemical analysis was used to detect expression of the differentiation markers cytokeratin (CK)10, CK14, loricrin and peroxisome proliferator-activated receptor alpha (PPAR-α), and of the EMT markers E-cadherin and N-cadherin in normal limb and body skin, and biopsies from limb and body wounds. Results: Loricrin and CK10 were expressed in normal skin and periwound skin but not in migrating epithelium of body and limb wounds. However, they reappeared at the migrating epithelial tip of body wounds only. CK14 and PPAR-α had uniform distribution throughout the migrating epithelium. N-cadherin was not expressed in normal unwounded skin but was detected in periwound skin adjacent to the wound margin. E-cadherin expression decreased at the wound margin. Conclusions and clinical importance: Presence of N-cadherin suggests that cadherin switching occurred during wound healing, this may be an indication that EMT occurs in horses. To the best of the authors’ knowledge, this has never been described in horses before and warrants further investigation to assess the clinical implications. The tip of the migrating epithelium in body wounds appeared more differentiated than limb wounds, which could be part of the explanation for the superior healing of body wounds.