Abstract.Objectives.  To evaluate the relationship of Lewis genotypes with major cardiovascular risk factors and the intima‐media thickness (IMT) of carotid arteries. Lewis genotyping included four major mutations of the Lewis (FUT3) gene at nucleotide positions 59, 1067, 202 and 314.Design.  Two complementary population‐based cross‐sectional studies.Setting.  The Atherosclerosis Risk in Communities (ARIC) Study.Subjects.  The relationship between Lewis genotype and major cardiovascular risk factors was studied in 761 men and women aged 45–64 years without known clinical atherosclerotic disease; 577 were Caucasians and 184 were African‐Americans. The association of Lewis genotype and subclinical carotid atherosclerosis was studied in 419 individuals with, and 819 controls without carotid IMT of >1.0 mm, measured by B‐mode ultrasound.Main outcome measures.  Mean values of cardiovascular risk factors by Lewis genotype. Lewis genotype frequencies in subclinical carotid atherosclerosis cases and controls.Results.  Individuals with Lewis genotypes consistent with lack of α(1,3/1,4)‐fucosyltransferase activity (i.e. Lewis‐negative genotype) had statistically significantly lower fasting glucose, factor VIIIc, von Willebrand factor and diastolic blood pressure compared with their counterparts with Lewis‐positive genotypes. The distribution of Lewis genotypes and haplotypes was not significantly different between individuals with carotid IMT of >1.0 mm (cases) and their controls. The odds of carotid atherosclerosis in carriers of the Lewis‐negative genotype was 1.23 (95% confidence interval 0.70–2.16) compared to individuals with Lewis‐positive genotype, controlling for age, gender and race/ARIC field centre.Conclusion.  The lack of a statistically significant association between Lewis ‘genotype’ and subclinical atherosclerosis in our data suggests that earlier studies reporting associations at the ‘phenotypic’ level may reflect aspects of the biology of the Lewis system other than an inherent genetic property.