Background: Non-syndromic cleft lip and palate (NSCLP) is considered a congenital structural anomaly of complex etiology. The history of inheritance type and genes related to dental anomalies and NSCLP, interfere with normal craniofacial development. Aim: To identify the presence of AXIN2 and MSX1 mutations associated with dental anomalies in patients with NSCLP. Method: Exploratory analytical observational study. The population of reference was conformed by 18 families (Trios: mother, father and probands) of Bogota (Colombia). The age range of the probands was 6 to 17 years, with diagnosis of FLPNS and dental anomalies. The clinical evaluation was performed and panoramic radiographs were analyzed to identify dental anomalies. Mutations of the AXIN2 and MSX1 genes were identified from saliva and genotyping samples. The phi coefficient and the chi-square test were applied for the statistical analysis. Results: AXIN2 proved to be the gene with the greatest association with NSCLP. The most frequent dental anomalies in individuals with NSCLP were agenesis and microdontia. The MSX1 gene demonstrated association with the presence of dental anomalies (agenesis and microdontia). Segregation of the AXIN2 gene from mothers to their offspring with NSCLP (p = 0.004 ;;) was demonstrated. No association was found between the mutation of the AXIN2 gene and the presence of dental anomalies in children with NSCLP. Conclusions: The presence of the mutation in the AXIN2 gene was frequent in individuals with NSCLP and in individuals with agenesis and microdontia.