Studies investigating the association between gene polymorphisms involved in homocysteine/folate metabolism and Down syndrome (DS) have reported contradictory or inconclusive results. A meta-analysis of 11 case-control studies relating MTHFR C677T, MTHFR A1298C and MTRR A66G gene polymorphisms to the maternal risk of DS was carried out. For MTHFR C677T polymorphism the heterogeneity between studies was significant (P=0.03) and the random effects (RE) pooled odds ratio (OR) was not significant: RE OR=1.18 (0.99-1.40). The recessive model for allele MTHFR 677T showed nonsignificant heterogeneity overall (P=0.21) and the association was not significant: fixed effects (FE) OR=1.27 (0.98-1.64). However, sensitivity analysis changed the pattern of results and the association became marginally significant [FE OR=1.31 (1.01-1.71)]. The dominant model showed no association. Finally, statistically significant associations between the MTHFR A1298C and MTRR A66G gene polymorphisms and the risk of DS were not found. The cumulative meta-analysis of MTHFR C677T showed a trend toward an association as the amount of data increased, and the recursive cumulative meta-analysis indicated that there was insufficient evidence for claiming or denying an association for all gene polymorphisms. In addition, there was no difference between the magnitude of effect observed in large versus small studies. Large and rigorous case-control studies that investigate gene-gene and gene-environment interactions need to be performed before conclusive claims about the genetics of DS can be made.