Metabolic syndrome (MetSy) is characterized by the presence of obesity, hypertension, altered glucose metabolism, and/or increased non-HDL cholesterol. This study aimed at elucidating the association between obesity with subclinical target organ damage and biochemical parameters included in MetSy pathogenesis. This study included 130 apparently healthy subjects. Plasma levels of oxidized-LDL-cholesterol (ox-LDL-Chol), nitric oxide (NO) metabolites, inducible NO synthase (iNOS), and plasminogen activator inhibitor-1 (PAI-1) were measured. Non-invasive assessment of liver disease included fatty liver index (FLI) and nonalcoholic fatty liver disease (NAFLD) fibrosis score. Carotid artery plaques were assessed by color Doppler imaging. A total of 65 patients with MetSy were included in the MetSy group, while 65 without MetSy entered the control group. Ox-LDL-Chol levels were higher in the MetSy group compared to the control group, regardless of obesity. Levels of NO metabolites were similar in obese and non-obese patients with MetSy, but lower than in the control group. Obese patients with MetSy had higher iNOS values compared to non-obese ones, with similar PAI-1 levels. NAFLD was present in all obese patients with MetSy compared to 70% of non-obese subjects. Hypertension, higher values of waist-to-hip ratio, PAI-1, and remnant cholesterol were associated with NAFLD. Finding of asymptomatic carotid plaques was associated with patients' age, hypertension, and higher waist-to-hip ratio. MetSy and obesity significantly alter the levels of NO metabolites, iNOS, ox-LDL-Chol, and PAI-1. High prevalence of NAFLD in obese patients with MetSy requires active screening and treatment of potential risk factors.