In unilateral cleft lip affected tissue, a statistically significant strong correlation (Spearman’s rho (rs) = 0.6–0.8) was notified between the number of PAX9-containing epitheliocytes in the epithelium and the number of PAX9-containing cells within the connective tissue (rs = 0.618, p < 0.001). This evidence concerns the gene PAX9 and cleft lip.