Introduction Information on microscopic anatomy of equine skin is sparse. In horses, limb wounds often become chronic and/or non-healing whereas body wounds heal normally. These dissimilarities in healing patterns might be a product of different phenotypic characteristics of body and limb skin. The objective of this study was to investigate microscopic anatomy, epidermal thickness, keratinocyte proliferation and differentiation as well as the presence of mast cells in normal equine skin of body and limb. Materials and methods The study involved body and limb skin biopsies from six horses. Histological characteristics of the epidermis were assessed and epithelial thickness measured. Immunohistochemistry was performed to investigate epidermal differentiation patterns of cytokeratin (CK) 10, CK14, CK16, loricrin, and peroxisome proliferator-activated receptor alpha (PPAR-α), epidermal proliferation (Ki-67 immunostaining), and mast cells distribution in the skin. Results The epidermis was significantly thicker in the limb skin compared to body skin (p < 0.01). Epidermal proliferation and CK distribution did not show differences in the two anatomical areas. Loricrin presence was focally found in the spinous layer in four out of six limb skin samples but not in body skin samples. Tryptase positive mast cells were detected in the dermis and their density (cell/mm2) was not different between body and limb. Discussion and conclusion Here we report for the first time about the normal distribution of CK10, CK14, CK16, PPAR-α, and loricrin in equine limb and body skin as well as about epidermal proliferation rate and mast cell count. It will be relevant to investigate the distribution of the investigated epithelial differentiation markers and the role of mast cells during equine wound healing and/or other skin diseases.