Non syndromic clefting has always been thought of being a multifactorial inheritance with the role of a major Gene . Recently the MSX1 gene has been implicated in the cause of non syndromic clefting . The aim of this study was to understand the role of the MSX 1 gene in non-syndromic clefting in South Indian Population .The Study proved the lack of any mutation in MSX 1 gene unlike its association in some caucasian population . This study also establishes the variability of the etiological factors to Non syndromic clefting in the world.