This study aims to determine the prevalence of dental anomalies and MSX1 gene 799G>T polymorphism and its association with non-syndromic cleft lip with or without palate (NSCLP) attending Hospital Universiti Sains Malaysia. Clinical and radiological assessments on 37 NSCL±P patients and 80 non-cleft children were done to detect dental anomalies. The buccal cells were collected and polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP) was used to identify polymorphism. NSCL±P was higher among males (54%) and mostly unilateral cleft lip and palate (51.3%). The prevalence of dental anomalies in morphology in NSCL±P was 18.9% (95% CI: 5.7%, 32.2%) and non-cleft was 6.3% (95% CI: 0.8%, 11.7%). Hypodontia in NSCLP was 75% (95% CI: 61.2%, 90.2%) and non-cleft was 7.5% (95% CI: 1.6%, 13.4%). There was a significant association between NSCLP and anomalies in morphology (P= 0.04; OR=3.5)) and number (P< 0.01; OR= 40). There was an absence of rare 799G>T polymorphism in all NSCL±P and non-cleft children indicating that all samples contain common 799G polymorphism. In conclusion, the prevalence of dental anomalies in morphology and number was significantly higher in NSCL±P compared to non-cleft children. However, it was not significantly associated with MSX1 799G>T polymorphism.