Background: Obesity as a chronic polygenic condition has been a public health challenge for many years. Many scientific studies have focused on the study of the effects of excess weight on the state of the cardiovascular system (CVS). However, the effect of body composition on CVS, in particular on vascular endothelial function (EF) and heart rate variability (HRV), has not yet been clearly established. Methods: Women aged 25 to 60 years went under investigation of body composition parameters identified with Tanita BC-601 analyzers. Study of endothelial function was performed using rheograph “ReoCom”. HRV was studied using electrocardiograph “CardioLab”. Results: There was a statistically significant difference between EF parameters before and after the body composition correction program in both models. However, the statistically significant effect of body composition parameters on the EF index was only found in the first model. In addition, the first model showed noticeable influence of the parasympathetic system on the EF and significant changes in these indicators after the correction program. Conclusion: Using only the BMI to examine the effect of overweight on endothelial function, it is possible to miss the significant impact of visceral fat on the state of the endothelium. Also, it is possible to overlook the effect of correcting body composition on HRV and EF. Women should be recommended to correct body composition in order to prevent risk of low parasympathetic activity resulting in CVD. Correction also serves as a therapeutic purpose in early stage correction of endothelial dysfunction linked to CVD.