Background TheS-adenosyl-methionine (SAM) availability is crucial for DNA methylation, an epigenetic mechanism involved in nonsyndromic cleft lip with or without cleft palate (NSCL/P) expression. The aim of this study was to assess the association between single-nucleotide polymorphisms (SNPs) of genes involved in SAM synthesis and NSCL/P in a Chilean population. Methods In 234 cases and 309 controls, 18 SNPs inAHCY,MTR,MTRR, andMAT2Awere genotyped, and the association between them and the phenotype was evaluated based on additive (allele), dominant, recessive and haplotype models, by odds ratio (OR) computing. Results Three deep intronic SNPs ofMTRshowed a protective effect on NSCL/P expression: rs10925239 (OR 0.68;p = 0.0032;q = 0.0192), rs10925254 (OR 0.66;p = 0.0018;q = 0.0162), and rs3768142 (OR 0.66;p = 0.0015;q = 0.0162). Annotations in expression database demonstrate that the protective allele of the three SNPs is associated with a reduction ofMTRexpression summed to the prediction by bioinformatic tools of its potentiality to modify splicing sites. Conclusions The protective effect against NSCL/P of these intronicMTRSNPs seems to be related to a decrease in MTR enzyme expression, modulating the SAM availability for proper substrate methylation. However, functional analyses are necessary to confirm our findings. Impact SAM synthesis pathway genetic variants are factors associated to NSCL/P. This article adds new evidence for folate related genes in NSCL/P in Chile. Its impact is to contribute with potential new markers for genetic counseling.