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MTHFR C677T polymorphism and hyperhomocysteinemia have been associated with congenital malformations of the heart and neural tube defects. A common missense mutation in the MTHFR gene (C to T substitution at position 677) produces a variant with reduced enzymatic action.The aim of this retrospective case control study was to investigate whether the occurrence of the MTHFR polymorphism is increased in mothers and fathers of children with a congenital heart disease (CHD) in our population.We genotyped 31 couples with CHD offspring and 31 control couples for this study by obtaining smears from buccal gingiva cells and analyzed these for the MTHFR polymorphism by hybridization on microarrays.Statistical significance was calculated using the χ-square test and Pearson-exact test, respectively. The prevalence of homozygosity or heterozygosity for the MTHFR polymorphism was not significantly increased in parents of CHD affected children. Nevertheless significance was observed for the association between aortic arch anomalies and the mothers.The results of this study do not show any significant association between the MTHFR C677T polymorphism and CHD in our population. Although the numbers are small (n= 3), the MTHFR (C677T) polymorphism may be linked to the development of aortic arch anomalies.