Aim. To examine contribution of polymorphisms of genes of endothelial NO-synthase (eNOS), NADPH-oxidase and methylenetetrahydrofolate reductase (mTHFR) to development of remodeling of cardiovascular system and chronic disease of the kidneys (CDK) in patients with metabolic syndrome (mS) and obesity. Material and methods. Standard clinical and device examinations were made and polymorphisms C242T of gene of subunit p22-phox of NADPH-oxidase, G894T of gene of eNOS and C677T of gene of MTHFR were studied in 66 MS patients (49 males and 17 females, age 19-62 years. Results. The presence of even one prognostically poor allele variants of the genes studied was registered in 83 examinees. The genotype 242TT p22-phox of NADPH-oxidase subunit was associated with the highest insulin resistance, allele 894T of gene eNOS - with reduced glomerular filtration rate and progression of left ventricular hypertrophy. Conclusion. Polymorphism of the genes the products of which modulate endothelial function can be considered as potential predictors of severity of MS target organs impairment.