A comparative analysis of gene expression profiles of carotid atherosclerotic plaques and intact internal thoracic arteries of patients with advanced atherosclerosis was performed by using the Human-12 BeadChip Microarray (Illumina, USA). The most down-regulated genes in the carotid atherosclerotic plaques were APOD, FABP4, CIDEC, and FOSB, in contrast, up-regulated gene was SPP1 (|FC| > 64; pFDR < 0.05). The majority of differentially expressed genes were down-regulated in advanced atherosclerotic plaques. For example, genes involved in immune and inflammatory responses (arachidonic acid metabolism, cytokine-cytokine receptor interaction, NOD-like receptor signaling pathway, Jak-STAT signaling pathway, TNF signaling pathway) were down-regulated in advanced atherosclerotic plaques as compared with the healthy arteries. The most significant biological process of genes down-regulated in carotid atherosclerotic plaques (compared to intact internal thoracic arteries) was “cellular response to metal ions” (metallothioneins), and for upregulated genes was the organization of the extracellular matrix.