Purpose: The primary goal of this research study was to determine the plasma levels of folate, vitamin B, and homocysteine in malnourished children in Uttar Pradesh-India, and also to evaluate the 5, 10- methylenetetrahydrofolate reductase (MTHFR) 677C>T mutation in the MTHFR gene as nutrigenetic factors in the children with malnutrition. Methods: 345 samples were collected to assess the fasting plasma levels of folate, vitamin B, and homocysteine using an ELISA. A polymerase chain reaction (PCR) with specific primers was used to analyze the MTHFR 677C>T polymorphism, followed by amplicon digestion with the Hinf I restriction enzyme (C677T genotypes were determined by PCR–RFLP). Results: Compared to controls, the malnourished group had higher plasma homocysteine levels and lowered folate and vitamin B12 levels (P<0.001). The CC genotype was present in 26 out of the 167 malnourished children, followed by CT in 52 and TT in 89. CC, CT, and TT genotype frequencies were 15.56%, 31.13%, and 53.29% respectively. In the malnourished group, the frequency of C allele was 0.31, and T allele was 0.68. Genotype frequencies in the control group: CC was observed in 162 (91.01%), CT in 14 (7.86%), and TT in 2 (1.12 %). In control, the C allele was found to have a frequency of 0.94, while the T allele had a frequency of 0.05. Conclusion: In short, the percentage of homozygous genotype (TT) is highest in malnourished children associated with a high level of homocysteine which shown the deficiency of folate and vitamin –B. However, childhood malnutrition may be caused by gene-environment interactions as well as nutrient deficiencies. Nutrient absorption and metabolism may be affected by genetic polymorphisms in host genes. Therefore, it is important to investigate the genetic predisposition to malnutrition, identify genetic markers and biomarkers that can aid in the identification of children at risk of malnutrition, and investigate new treatment modalities that can help in the clinical management and treatment of malnourished children. Question: Is risk of congenital impairment associated with mutated MTHFR and deficiency of folate, vitamin B12 and high level of homocysteine in malnourished children. Finding: Yes mutated MTHFR have shown polymorphism C667T with low folate and vitamin B12 and high level of homocysteine. Significant associated with malnourished children. Meaning: MTHFR gene is nutrigenetic factors associated with nutrient and interact with nutrients through the specific mode of action.