Trisomy 21 is the most common chromosome abnormality characterized by the presence of three copies of chromosome 21 in the genome. The clinical disorder attributed to trisomy 21 is Down syndrome. Patients with Down syndrome are heterogeneous in their phenotypic expression. Due to the location of the cystathionine b-synthase gene on chromosome 21, and its involvement in one carbon metabolism, homocysteine levels have been found to be decreased in children with Down syndrome. The study of the regulation of one carbon metabolism in Down syndrome becomes important in light of possible normalization of the metabolic imbalance and the detection of increased sensitivity to therapeutic interventions. Thus, the importance of evaluating single nucleotide polymorphisms in genes involved in one carbon metabolism need to be addressed in individuals with trisomy 21. This review offers an analysis of the impact of these polymorphisms in Down syndrome and their possible implications for phenotypic heterogeneity.