Polycystic ovary syndrome (PCOS) is the most common endocrine condition affecting 6–18% of adolescents and is strongly associated with obesity and cardiovascular risk factors, enhancing the risk of atherosclerosis. Thirty-two adolescents with newly diagnosed PCOS were evaluated for lipid profile disorders, insulin resistance, inflammation, non-alcoholic fatty liver disease (NAFLD), and subclinical atherosclerosis through measurements of carotid intima–media thickness (cIMT). The relationships of the above markers with increased body mass index and abdominal obesity were investigated. Twenty-three adolescents (72%) were overweight (OW) or obese (OB). The OW/OB group had significantly higher insulin, HOMA-IR, high-sensitive C-reactive protein (hsCRP), visceral adiposity index (VAI), and lipid accumulation product (LAP) levels; and lower glucose-per-insulin ratios and HDL-C levels compared to the healthy weight group. The cIMT and small dense low-density lipoprotein cholesterol (sdLDL-C) levels did not differ between the two groups. Similarly, cIMT and sdLDL-C levels did not differ between PCOS-adolescents and healthy controls. CIMT was positively correlated with systolic blood pressure and waist circumference per height ratio. In conclusion, OW/OB PCOS-adolescents have a cluster of adverse factors predisposing them to atherosclerotic cardiovascular disease. Therefore, early cardiovascular risk assessment, as well as timely and targeted interventions, are necessary for prevention.