We studied the interaction between the indicators of lipid exchange and thyroid status among the inhabitants of radiation contaminated territories under additional psycho-emotional load. We observed 170 students aged between 18–24 and divided them into a control group of students who were from areas unaffected by radiation (70 people) and the main experimental group of students from territories of increased radio-ecological load (IV radiation zone, 100 people). We determined the content of thyrotropic hormone (TTH), triiodothyronine (T3), thyroxin (T4), total cholesterin (TC), triglycerides (TG), cholesterin of lipoproteins of high density (Ch-LPHD) and cholesterin of lipoproteins of low density (Ch-LPLD). We found that people who had lived since birth in territories which were contaminated with radionuclides and were affected by prolonged influence of small doses of ionizing radiation had significant fluctuations of indicators of concentrations of TTH, T3 and T4, forming manifestations of hypothyroidism and hyperthyrosis among some of those tested. Independently from hyperthyrosis, the effect was accompanied by growth in the level of TH, TG, Ch-LPHD and Ch-LPLD. Persons with manifestations of hypothyroidism had the content of TH above the upper limit of the homeostatic norm and the level of Ch-LPLD was higher than the norm in sub-groups with features of hypo- and hyperthyrosis. All those tested from the main group showed a significant positive correlation connection between the level of TTH and levels of TH and Ch-LPLD. The subgroup with manifestations of hyperthyrosis had a positive correlation between the levels of TTH and TG, the subgroups with manifestations of euthyroidism and hyperthyrosis had a negative correlation between the levels of TTH and Ch-LPHD. The hyperthyrosis subgroup had a significant positive correlation connection between T3 and TH and Ch-LPLD. The euthyroidism and hypothyroidism subgroups had a significant negative correlation between T3 concentration and Ch-LPLD. The cortisol indicator positively correlated with levels of TH and Ch-LPLD in all subgroups divided according to thyroid status. In the conditions of additional psycho-emotional load (examinations), those tested had an increased level of TP (higher than the norm in the subgroups of hyperthyrosis and hypothyroidism) caused by the increase in cortisol level and a tendency of decrease in TTH. At the same time, the level of Ch-LPLD increased (higher than the upper norm) as a result of decrease in the content of Ch-LPHL. The coefficient of correlation between the level of TTH and levels of TH and Ch-LPLD lost statistical significance in all subgroups divided according to thyroid status. In the hyperthyrosis subgroup, the effect of loss of correlation with TH and Ch-LPLD was also observed for T3. Thus, the individuals tested from territories polluted by radionuclides, had proaterogenic changes dependant on thyroid status,which can become a precondition for the development of metabolic syndrome. The risk of dyslipidemia increases in the conditions of additional psycho-emotional load, when the regulatory effect of the thyroid gland`s hormones is reduced.