<h4>Objective</h4>This study aimed to investigate the association between variants present in the MSX1 gene and the risk of developing non-syndromic cleft lip with or without cleft palate (NSCL±P) among individuals of Malay ethnicity in Malaysia.<h4>Materials and methods</h4>This case-control study involved 89 patients with NSCL±P and 100 healthy control subjects. Here, MSX1 is linked to cleft palate.