The inconsistency of data regarding intrauterine programming of cardiovascular risk factors may be largely caused by genetic predisposition and later lifestyle. We analyzed whether low birth weight and apolipoprotein E (Apo E) polymorphism participate in the onset of hypercholesterolemia in children. Our approach was based on hypothesis that genetically enhanced susceptibility of different individuals might influence the effects of intrauterine programming. Two groups were selected from 2000 children at the beginning of an ongoing study: high-cholesterol group (HCG, n=67) and low-cholesterol group as a control (LCG, n=72). Both groups were divided into tertilles according to birth weight and we compared birth weight and apo E gene polymorphism between and within groups. The birth weight in HCG was 0.3 kg lower than the controls (p<0.001). The frequency of apoE4 was 31 % in HCG and only 10 % in LCG. The frequency of apoE4+ genotypes was not significantly different between tertilles based on birth weight in HCG. We suppose that intrauterine undernutrition, demonstrated by a lower birth weight, participates in the development of hypercholesterolemia already in childhood. The effects of low birth weight and the candidate gene - apoE, are synergic.