Given the limited literature available on gene–diet interaction, and specifically on maternal folic acid intake and its relationship with the global methylation of genes associated with VSD (MTHFR, TBX1, TBX20, and AXIN1), this research aims to determine the relationship between maternal folic acid intake during pregnancy and the methylation status (MS) of genes associated with VSD. This evidence concerns the gene MTHFR and ventricular septal defect.