The significant immunoreactivity of PAX9 in the surface epitheliocytes and connective tissue cells of isolated cleft palate seems to emphasize the interaction between the epithelium and the underlying connective tissue in this specific type of cleft, which could affect tissue growth and remodeling during cleft formation, while the significant presence of PAX9 within the unilateral and bilateral cleft lip affected tissue and possible involvement in cleft pathogenesis within these specific types of clefts could not be excluded. Here, PAX9 is linked to cleft lip.