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Objective: The objective was to investigate the association between consanguinity and clefts in the craniofacial region. Materials and Methods: Sample consists of 179 non-syndromic cases of clefts in the craniofacial region and 200 healthy controls with no cleft or family history of clefting. A standardized questionnaire was prepared to investigate the information on the demographic characteristics and consanguinity. Chi-square and odds ratio were used to evaluate the risk of consanguinity in clefts in the craniofacial region. Results: There is a significant association between consanguinity and clefts (P = 0.001) when comparing the consanguinity and no consanguinity in cleft group and non-cleft group, and the association is more with the second degree consanguinity than the third degree consanguinity. Conclusion: Consanguinity is a risk factor for clefts in the craniofacial region.