Some investigations have demonstrated that a combined endurance–strength training is the most effective in the treatment of obesity. The aim of the research was to access how different trainings influence: endothelial function, lipid metabolism, and risk of atherosclerosis in women with obesity. In a randomized trial, 39 obese women aged 28–62 completed endurance (n = 22, 60-80% HRmax) or combined training (n = 17, 20 minutes of strength exercises, 50–60% 1RM and 25 minutes of endurance training, 60-80% HRmax). Before and after the intervention vascular endothelial function (endothelial nitric oxide synthase (eNOS), vascular endothelial growth factor (VEGF), thiobarbituric acid reactive substances (TBARS), blood total antioxidant capacity (TAC)), total cholesterol, low-density lipoprotein cholesterol (LDL-C), high-density lipoprotein cholesterol (HDL-C), triglycerides and C-reactive protein (CRP)as well as visceral adiposity index (VAI), total-body skeletal muscle mass and atherogenic index of plasma (AIP) were determined. After the trainings, in both groups total cholesterol and total-body skeletal muscle mass increased (p < 0.05). In the group undergoing combined training, lower (p < 0.05) VAI, AIP, CRP and LDL-C were noted. In the group undergoing endurance training TBARS concentration decreased (p < 0.01), while the HDL-C (p < 0.01) concentration as well as eNOS (p < 0.05) activity increased. No significant differences between groups were found, either before or after the programs. Both training programs led to the improvement of lipid metabolism, but only endurance training alone favorably changed indicators of endothelial functions in women with obesity.