Till now, the management of autoimmune thyroid diseases (AITD) depends on symptomatic treatment and replacement or anti-thyroid therapy. Uncovering the pathophysiologic mechanisms of autoimmunity provides hope for new insights into management. These new treatments aim to modulate the immune reaction and stop the autoimmune process. T regulatory cells (Tregs) are central in antagonising autoimmunity. This study aimed to compare the number of CD4/CD25/FOXP3 T regulatory cells in the different forms of autoimmune thyroid diseases and in the normal population, and to compare the number of CD4 + CD25 + FOXP3 + T regulatory cells between the different forms of AITD, HT, and GD. Also, to investigate the difference in the number of CD4/CD25/FOXP3 T regulatory cells in AITD associated with allergic disorders on one hand and autoimmune thyroid diseases not associated with allergic disorders on the other hand. This study included 18 patients suffering from Hashimoto’s thyroiditis (HT), 15 patients suffering from Graves’ disease (GD); and, for comparison, the Tregs level was measured in 15 healthy control patients. A statistically significant decrease was found regarding CD4/CD25, CD25/FOXP3 percentages and CD4/CD25/FOXP3 absolute number between patients of AITD and the normal population. The absolute number of CD4/CD25/FOXP3 was lower in the GD group than in HT group. Allergic comorbidities do not influence Tregs percentage or their CD4/CD25/FOXP3 absolute number in any of the AITD forms. Tregs may be a potential therapeutic target for AITD.