Our work aimed to study the influence of cholecalciferol on neurogenesis, neurotrophins and their receptors pathway-focused genes expression in patients with autoimmune thyroiditis and hypothyroidism. The pathway-specific PCR array (Neurotrophins and Receptors RT2 Profiler PCR Array, “QIAGEN”, Germany) was used to identify and validate the neurogenesis regulatory genes expression in patients with thyroid pathology and control group. The results showed that in patients with autoimmune thyroiditis-caused primary hypothyroidism, the expression of BDNF, FAS, FGF2, HSPB1, IL10, NGF, NGFR, NRG1, NTF3, NTF4, TGFB1, and TP53 were increased after treatment with cholecalciferol and L-thyroxine. The mRNA levels of BAX, GDNF, CD40, FOS, GDNF, GFRA1, IL1B, and STAT3 were significantly decreased in patients with autoimmune thyroiditis-caused primary hypothyroidism after treatment with cholecalciferol and Lthyroxine compared to the patients who received only L-thyroxine. Therefore, the addition of vitamin D to standard therapy alters the transcriptional profile of blood cells in patients with primary hypothyroidism.