Estrogens protect from endothelial dysfunction as well as affect lipid metabolism and certain polymorphisms in the ERα gene have been associated with coronary disease in earlier studies. IL-6 plays a central role in the inflammation process, and polymorphism of the IL-6 gene as well as plasma concentrations of IL-6 and CRP, were also associated with ACS in previous studies. Endothelial function can be assessed non-invasively on peripheral arteries, using the FMD test. The aim of this research was to analyze the association of ERα gene polymorphism (T/A repeat length) and IL-6 gene polymorphism (174G>C) in the offspring of patients with early coronary disease and endothelial dysfunction using the FMD method. This study analyzed the prevalence of these polymorphisms in both populations, as well as the association of ERα gene polymorphism with pathological lipidogram values, as well as the association of IL-6 gene polymorphism with pathological plasma CRP values. Study showed a high incidence of heterozygous and homozygous "long" allelic forms of the ERα polymorphism in patients with early coronary disease - in as many as 76% of them, and a high incidence of heterozygous and homozygous allelic forms of the IL-6 polymorphism, present in 56% of patients. This study is the first to investigate the frequency of these polymorphisms in the children early coronary patients, and found them in 78% for the ERα polymorphism and 66% for the IL-6 polymorphism. Also, the "short" allelic form of the ERα polymorphism ("wild" type) in our study had an impact on plasma lipid values in male patients and male offsprings, who had significantly higher LDL values. Likewise, the presence of homozygous and heterozygous allelic forms of the IL-6 polymorphism was associated with increased CRP values in 32% of patients with early coronary disease compared to 18% with the "wild" type. The offspring of patients with early coronary disease who inherited both homozygous forms of the ERα and IL-6 polymorphisms had the lowest measured FMD values with a median twice as low as the offspring with the "wild" type of both polymorphisms. In conclusion, this study supports the possible role of ERα and IL-6 polymorphism in the endothelial dysfunction detected with FMD, but additional studies are needed in order to investigate their potential use as a biomarker of early coronary disease.