Background: Hypothyroidism is a common condition with potentially devastating health consequences that spread worldwide. Stems cells (SCs) based therapy had showed promising benefits in treatment of many diseases on animal models and applied on some human clinical issues. Aim of Study: To investigate the effect of bone marrow mesenchymal stem cells (BM-MSCs) on the biochemical and histological structures of the thyroid gland after experimentally induced hypothyroidism in adult male albino rats. Material and Methods: Forty five adult male Sprague-Dawley albino rats were divided into 3 equal groups: Control group (Group I), Hypothyroidism induced group (Group II); received orally carbimazole 45mg/kg of rat/day for 5 days/week for 4 weeks and Induced hypothyroidism treated with BM-MSCs group (Group III); received oral dose of carbimazole 45mg/kg of rat/day for 5 days/week for 4weeks then received single intravenous injection of 1x10 6 cells of BM-MSCs. This group was subdivided into three equal subgroups according to the time of scarification; Subgroup III6: Scarified at the end of 6th week, Subgroup III8: Scarified at the end of 8 th week and Subgroup III10: Scarified at the end of 10 th week. At the end of the experiment, the hormones of thyroid function were measured and histological examination of the thyroid tissue were done. In addition to morphometric study and statistical analysis. Results: BM-MSCs injection to the induced hypothyroidism rats showed that after 6 and 8 weeks, there were highly significant increase (p<0.01) of freeT3 and T4 values and highly significance decrease of TSH compared to the induced hypothyroidism group. On the other hand, after 10 weeks from injection of BM-MSCs, there were insignificant differences (p>0.05) of free T3, T4 and TSH compared to the induced hypothyroidism group. The histological examination of the induced hypothyroidism after 6 weeks of BM-MSCs injection showed variable degree of response. However, after 8 weeks of BM-MSCs injection, there was universal improve