Aim: Embryonic tumors are associated with an interruption during normal organ development; they may be related to disturbances in the folate pathway involved in DNA synthesis, methylation, and repair. Prenatal supplementation with folic acid is associated with a decreased risk of neuroblastoma, brain tumors, retinoblastoma, and nephroblastoma. The aim of this study was to investigate the association between MTHFR rs1801133 (C677T) and RFC-1 rs1051266 (G80A) genotypes with the risk of developing nephroblastoma and neuroblastoma. Materials and Methods: Case-mother/control-mother dyad study. Samples from Brazilian children with nephroblastoma (n = 80), neuroblastoma (n = 66), healthy controls (n = 453), and their mothers (case n = 93; control n = 75) were analyzed. Genomic DNA was isolated from peripheral blood cells and/or buccal cells and genotyped to identify MTHFR C677T and RFC-1 G80A polymorphisms. Differences in genotype distribution between patients and controls were tested by multiple logistic regression analysis. Results: Risk for nephroblastoma and neuroblastoma was two-to fourfold increased among children with RFC-1 polymorphisms. An increased four-to eightfold risk for neuroblastoma and nephroblastoma was seen when the child and maternal genotypes were combined. Conclusion: Our results suggest that mother and child RFC-1 G80A genotypes play a role on the risk of neuroblastoma and nephroblastoma since this polymorphism may impair the intracellular levels of folate, through carrying fewer folate molecules to the cell interior, and thus, the intracellular concentration is not enough to maintain regular DNA synthesis and methylation pathways.