ObjectiveThis study aims to determine if 5,10‐methylenetetrahydrofolate reductase (MTHFR C677T and A1298C) and methionine synthase reductase (MTRR A66G) gene polymorphisms were associated with fatty acid (FA) levels in mothers of fetuses with neural tube defects (NTDs) and whether these associations were modified by environmental factors.MethodsPlasma FA composition was assessed using capillary gas chromatography. Concentrations of studied FA were compared between 42 mothers of NTDs fetuses and 30 controls as a function of each polymorphism by the Kruskal–Wallis nonparametric test.ResultsIn MTHFR gene C677T polymorphism, cases with (CT + TT) genotype had lower monounsaturated FAs (MUFA) and omega‐3 polyunsaturated FA (n‐3 PUFA) levels, but higher omega‐6 polyunsaturated FAs (n‐6 PUFA) and omega‐6 polyunsaturated FAs: omega‐3 polyunsaturated FAs (n‐6:n‐3) ratio levels. In MTRR gene A66G polymorphism, cases with (AG + GG) genotype had lower MUFA levels, but higher PUFA and n‐6 PUFA levels. Controls with (AG + GG) genotype had lower n‐6 PUFA levels. In MTHFR gene C677T polymorphism, cases with smoking spouses and (CT + TT) genotype had lower MUFA and n‐3 PUFA levels, but higher PUFA, n‐6 PUFA, and n‐6:n‐3 ratio levels. Cases with (CT + TT) genotype and who used sauna during pregnancy had lower n‐3 PUFA levels. In MTRR gene A66G polymorphism, cases with (AG + GG) genotype and who used sauna during pregnancy had higher PUFA and n‐6 PUFA levels.ConclusionsFurther research is required to clarify the association of FA metabolism and (MTHFR, MTRR) polymorphisms with NTDs.