The C/T-13910 LCT is closely associated with lactase persistence and LCT has emerged as a new candidate gene for obesity, in particular in northern Europeans. The aim of this research is to investigate to what degree sex determines the association between the LCT variant and anthropometric traits in a cohort of healthy individuals. We recruited 1000 (500 males and 500 females aged 18–65 years) healthy blood donors. The C/T-13910 LCT polymorphism was genotyped using TaqMan assays. All individuals were phenotyped with respect to anthropometric characteristics. Prevalence of genotypes was 22.7% CC (lactase non-persistent, LNP), 58.6% CT, and 18.7% TT. LNP genotype was present less frequently among men p = .0005; OR 0.582 [0.425–0.794]. Therefore, in addition statistical calculations were performed separately for men and women. Additional analysis demonstrated an association between the CC genotypes and higher chest ( p = .03), waist ( p = .005), and forearm circumference ( p = .0004) or more lean body mass ( p = .04), than T-allele carriers in males. In females, they were not significantly different. Men consumed more milk ( p = .003), while women ate more yoghurt ( p = .001). Pearson’s correlation analysis showed that the higher intake of milk and dairy products was associated with higher fat body mass among men with lactase persistence. In Caucasian men, the LNP genotype is associated with reduced milk intake and dairy products, but more fat-free mass and higher forearm circumference, which may be relevant to dietary management for lactose intolerant.