Elevated concentrations of the amino acid homocysteine and/or folate deficiency have been reported to affect neural development/function in both human patients and animal models. We have investigated the distribution of functional polymorphisms in genes involved in homocysteine/folate metabolism in children with high IQ and in children with average IQ. No differences in the frequencies of genetic variants in the methionine synthase or methylenetetrahydrofolate reductase genes were found. However, the cystathionine β-synthase (CBS) 844ins68 allele was significantly underrepresented in children with high IQ. The mechanism by which a functional genetic variant in the CBS gene may influence cognitive function remains to be determined.