This study was conducted on 21 male and female Egyptian patients with Nonsyndromic Cleft Lip with or without Cleft Palate aiming at exploring the presence of MSX1 gene mutation in Egyptian patients, after DNA extraction from 5 ml of peripheral blood, PCR amplification was carried and products were checked for successful amplification, Sequencing of exon I and II for the 11 cases was done then sequences were compared to the human sequences available via GENBANK accession number AF426432.1, two cases were found to have silent mutations (c.348C>T; p. G116G and c.543C>T; p.T181T) no change in amino acids, (p.G116G) Glycine is not changed, (p.T181T) Threonine is not changed, although the found mutations were silent, MSX1 gene mutations appear to have significant association with orofacial clefting.