Background: Nonsyndromic cleft lip with or without cleft palate (NS-CL/P) is one of the most common congenital anomalies and has a multifactorial etiology that involves both genetic and environmental factors. Objectives: The present study was aimed to evaluate the possible association between BHMT rs3797546 gene polymorphisms and NS-CL/P in a sample of Iranian population. Materials and Methods: This case-control study was performed on 100 NS-CL/P cases and 100 healthy controls. Tetra amplification refractory mutation system-polymerase chain reaction (T-ARMS-PCR) was used to detect the polymorphism. Analysis of data was done using χ2 test for categorical data, the associations between genotypes and NS-CL/P were estimated by computing the odds ratio (OR) and 95% confidence intervals (95% CI) from logistic regression analyses. Results: No significant difference was found between the groups regarding BMHT rs3797546 gene polymorphism. The C allele was not associated with NS-CL/P (OR = 1.27, 95% CI = 0.85-2.79, P = 0.690). Conclusions: Our data suggested that BMHT rs3797546 gene polymorphism was not associated with risk/ protection for NS-CL/P in a sample of Iranian population. Larger studies are required to validate our findings.