Metabolic syndrome (MetS) is associated with abnormal lipid metabolism, expressed by a higher level of triglycerides (TG) and lower levels of high-density lipoproteins (HDL). Lipid disturbances can be influenced by the intake of B vitamins or amino acids, in particular, folate or methionine and tryptophan. The metabolism of B vitamins and amino acids is related to folate metabolism cycle, which is limited by the MTHFR gene. People with an unfavorable genotype are characterized by a disturbed level of lipid profile and a higher level of homocysteine. Homocysteine is considered as an independent risk factor of cardiovascular disease. Therefore, the purpose of this study was to determine the relationship between amino acids and B vitamins intake, MTHFR genotype, lipid profile and atherogenic indices in postmenopausal women.The mean macronutrients, amino acids and B vitamins intake was evaluated by dietary records. Lipid profile and apolipoprotein A1 (ApoB) and B (ApoB) in serum were measured using the colorimetric method. Total homocysteine level (tHcy) in plasma were measured using high-performance liquid chromatography. MTHFR genotype analysis was performed with the use of single tube TaqMan SNP Genotyping Assay. Atherogenic indices, such as Castelliu2019s risk index I and II (CRI-I and CRI-II), the atherogenic coefficient (AC) and TG/HDL, were calculated.Women without MetS had lower levels of TG, VLDL, ApoB, CRI-I, CRI-II, AC and TG/HDL, and higher levels of HDL and ApoA1 than a woman with MetS. There were no differences in the concentrations of tHcy and Gsh and dietary intake. Additionally, MTHFR genotype and folate intake did not alter tHcy, lipid profile level, and atherogenic indices. Subjects with higher tHcy level (above the median value) had lower total protein intake, animal protein/plant protein ratio, protein/carbohydrates ratio levels and higher amino acids intake levels, e.g. methionine, lysine, arginine, glycine, and tryptophan, than subjects with lower tHcy level. Women who failed to meet their needs for B12 intake had 38.72% higher level of tHcy than women who met their needs.MetS is an independent factor associated with lipid profile and atherogenic indices in this study group. The MTHFR genotype or tHcy level in plasma has no effect on the lipid profile. However, vitamin B12 intake level may be a factor affecting the tHcy level, which is an independent risk factor for cardiovascular diseases.The project was financed by a National Science Centre award (decision number 2015/17/N/NZ9/04133).