A total of 523 subjects (297 females and 226 males) from the Canary Islands Nutrition Study (ENCA) were studied in order to examine the effect of the MTHFR 677C>T, 1298A>C and 1793G>A polymorphisms, adjusted for age, serum (S)‑folate and S‑cobalamin levels, on total plasma homocysteine concentrations (tHcy). Genotyping was performed with Pyrosequencing® technology. The MTHFR 677T‑allele was associated with increased tHcy concentrations only in males (P=0.005). The MTHFR 1298C‑allele was found to be associated with higher tHcy levels but similarly, only in males (P=0.025). The MTHFR 1793A‑allele was associated with decreased tHcy concentrations in the younger males (P=0.042). A haplotype‑based approach was marginally superior in explaining the genetic interaction of the MTHFR polymorphisms on tHcy plasma levels (R2 0.352 vs. 0.342 for a simple genotype‑based approach). A nutrigenetic interaction between the MTHFR 677C>T genotype and S‑cobalamin on tHcy levels was demonstrated in both genders. The increase in tHcy was more pronounced with decreasing S‑cobalamin quintiles in 677TT homozygotes (P=0.005 for males and P=0.015 for females) than with decreasing S‑folate quintiles (P for trend not significant). It was concluded that gene‑nutrient interactions may differ depending on the sex and age of the subjects. The transferability of gene‑nutrient interactions from one community to others may therefore be limited not only by different food patterns but also by different ages, genders and genotype distributions.