The relationship between subclinical hypothyroidism (SH) and Atherosclerotic (At) cardiovascular diseases (CVD) has been one of the most popular topics but causal connection between Hashimoto thyroiditis (HT), lipid profile and follicular epithelial molecular biology is controversial. We investigated 3 groups of patients (group I – HT, group II – HT+At, group III – At). All laboratory tests for thyroid function and lipid profile detection were used according to international guideline recommendations, coronary and femoral arteries intima-media thickness (IMT) were tested by high-resolution ultrasonography, thyroid gland histology and immunohistochemistry carried out by p63 and S100 protein expression control. The statistical analysis was performed using Microsoft Excel 7.0, SPSS-20 version, Mann-Whitney U-test and Pearson’s correlation. Comparisons between groups and factors were made using Multiple Linear Regression model. With the results obtained, dyslipidemia and the diastolic hypertension accelerate the hypothyroidism in HT+At group to predispose carotid and femoral arteries IMT. TSH and anti-TPO antibody levels are directly linked to the cardiovascular complications. Biomarkers S100 and p63 data show negative feedback effects of hypercholesterolemia on the high morphological risk features in Hashimoto parenchyma, which may partially explain the significant trend and pathobiological link of HT with Papillary thyroid carcinoma.