Thyroid hormone (TH) regulates metabolic pathways which may interfere with insulin action. There is limited knowledge on adipose tissue (AT) and skeletal muscle (SM) expression of genes associated with TH action in relation to insulin sensitivity. The aim of this study was to analyze AT and SM expression of the genes associated with TH action in subjects with different degree of insulin sensitivity and the regulation of these genes by insulin and free fatty acids (FFA). The study group comprised 72 euthyroid male subjects: 36 normal weight subjects and 36 overweight/obese subjects. Two-hour hyperinsulinemic-euglycemic clamp and tissue biopsies were performed. In the subgroup of 20 subjects, 9 normal weight subjects and 11 overweight/obese subjects, clamp was prolonged to 6 hours and another clamp with Intralipid/heparin infusion was performed after 1 week. Tissue biopsies were performed before and after each clamp. Overweight/obese subjects had higher AT DIO2, DIO3, and NCOR1, lower AT THRA and PPARGC1A, higher SM NCOR1, and lower SM DIO2, DIO3, PPARGC1A, and ATP2A2 expression. In AT, DIO2 and PPARGC1A increased, whereas NCOR1 and FOXO1 decreased after the clamp only in normal weight individuals. DIO3 decreased in both groups. In SM, NCOR1 decreased, whereas PPARGC1A and ATP2A2 increased after the clamp only in normal weight individuals. Tissue THRA and THRB decreased in both groups. Intralipid/heparin abolished these effects. Alterations in AT and SM expression of TH-related gene indicate a decreased tissue TH action in obesity. Inability to increase TH-related gene expression in obesity and during FFA oversupply may contribute to the aggravation of lipotoxicity.