The mutant alleles of the variants MTHFR C677T and, with less evidence, A1298C are associated with both elevated homocysteine plasma levels and vascular diseases arguing for hyperhomocysteinemia as a causal risk factor for vascular disease 
. However, there are inconclusive data that these MTHFR variants may questionably also be associated with smoking behaviour 
. Such an association would be an important confounder concerning the role of elevated homocysteine plasma levels as a vascular risk factor. In two selected cohorts, we analysed MTHFR C677T;A1298C haplotypes and observed that likelihood of being a smoker was lowest in those subjects homozygous for the wild-type-alleles677CC and 1298AA, while presence of a mutant allele increased the likelihood of being a smoker. MTHFR is expressed in the brain and is involved in remethylation of homocysteine to methionine, which can be activated to S-adenosylmethionine functioning as methyl group donor, e.g. for the synthesis of neurotransmitters and dopamine methylation 
. Whether an influence of MTHFR variants on such biochemical pathways may explain an association of these variants with smoking behaviour, remains speculative. Smoking is known to be associated with higher homocysteine plasma levels 
. Moreover, our data confirm that the T allele of MTHFR C677T and smoking interact in their association with homocysteine plasma levels, i.e. smoking homozygous T carriers had highest, non-smoking homozygous C carriers lowest homocysteine plasma levels 
Our study has several important limitations: Two heterogeneous study samples were retrospectively analysed. Both do not represent the normal population, but were recruited for studies on smoking cessation and atherosclerosis, respectively, which may have led to relevant selection bias as shown by the high rate of smokers. Controls did not completely match, thus, multivariate analyses were necessary. Further, such analysis of genotypes and smoking were initially not planned for sample 1, thus, information on smoking status was limited, i.e. “yes” versus “no” without clear definition. Further, we adjusted for age and sex, but other possible confounders like birth cohort effects and alcohol use were not regarded due to limited information. Results were only significant, if the two population samples were pooled, but only for trend or not in separate analyses, which would have been preferable due to the differences between those two samples. However, our data support to the theory that MTHFR C677T and smoking interact in generating elevated homocysteine plasma levels via unknown mechanisms. Such information may be relevant for the stratification of vascular risk factors. Moreover, our data suggest that MTHFR alleles with at least one of the mutant variants C677T and A1298C are associated with smoking. Published previous studies were inconclusive concerning such an association, which would be a relevant confounder concerning the association of MTHFR variants, hyperhomocysteinemia and vascular events. Speculatively, the difference between our findings – compared to prior negative results on associations between MTHFR genotype and smoking – may be due to analysing both variant regions C677T and A1298C simultaneously. Indeed, when C677T is analysed alone in our subjects, the difference between smokers and non-smokers was not significant. It may be justified that statistical strategies of future studies on the role of homocysteine metabolism in vascular disease regard such possible associations.