In the isolated cleft palate affected tissue, strong correlations (rs = 0.6–0.8) were detected between the number of PAX7-containing epitheliocytes within the epithelium and the number of RYK-containing cells in the epithelium (rs = 0.685, p < 0.001), between the number of PAX9-containing epitheliocytes in the epithelium and the number of PAX9-positive structures within the connective tissue (rs = 0.674, p < 0.001). Here, PAX9 is linked to cleft palate.