Cytokeratins (CKs) are intermediate filaments of epithelial cells. In humans, different types of epithelia as well as their neoplasms show distinct CK expression profiles. The aim of this study was to establish a panel of CKs for the identification of specialized canine epithelia that can be integrated in a routine diagnostic setting. Immunohistochemistry was performed on 42 formalin-fixed paraffin-embedded (FFPE) canine unaltered tissues including all epithelial tissues by using an antibody panel detecting CKs 7, 8, 13, 14, 17, 19 and 20 and the pancytokeratin marker AE1/AE3. Using this antibody panel, a differentiation scheme for the identification of canine tissues was developed. This allowed the identification of 23 out of the 42 examined canine tissues and the distinction of 9 groups of specialized epithelia. The statistical validation revealed high variations in the immunoreactivity for CKs 7, 8, 14, 17 and 20 between the donor dogs. The antibody detecting CK 7 (OV-TL 12/13) showed a decrease in immunostaining after a fixation time of 3 and 4 days. To the best of the authors' knowledge this is the first study that characterizes all canine epithelial tissues for their expression of CKs 7, 8, 13, 14, 17, 19 and 20 and the pancytokeratin marker AE1/AE3. Results of this study are an important prerequisite for comparative histology and for the investigation into similarities/differences of the cytokeratin expression between normal and neoplastic epithelia. Since this study was performed on FFPE tissue, it can be included in the workflow of a routine diagnostic laboratory.