Background/Aims: Congenital hypothyroidism (CH) in neonates is associated with lipid alterations that might be a risk factor for early cardiovascular disease in adult life. The aim of this study was to investigate the effect of CH on lipid metabolism and aortic intima media thickness (aIMT) as a unique finding of the increased risk of atherogenic risk in neonatal age. Methods: The study group consisted of 15 newborns with CH who were identified by neonatal mass screening (patient group), and 25 healthy newborns (control group). Serum lipid profiles and aIMT obtained from abdominal aorta were measured in all subjects. Results: The mean aIMT were higher in the patient group (0.46 ± 0.062 mm) compared with the control group (0.34 ± 0.035 mm; p = 0.006). The weight-adjusted aIMT of patients (0.13 ± 0.017 mm/kg) was also significantly greater than that of the controls (0.10 ± 0.019 mm/kg; p < 0.001). Total serum cholesterol levels were significantly higher in patients than those in healthy controls (130.80 ± 44.46 vs. 99.96 ± 18.87 mg/dl). The other lipid levels including triglyceride, low-density lipoprotein (LDL), high-density lipoprotein cholesterol and LDL cholesterol levels of the patients were slightly higher than those of the controls, without statistical significance. Conclusion: Neonates with CH have significantly higher aIMT with lipid alterations. Hypothyroidism might increase the risk of early atherosclerosis even in the neonatal period.