Purpose: This study was aimed to estimate the effect of bone marrow derived mesenchymal stem cells (BM-MSCs) on the submandibular salivary gland of induced hypothyroidism in rats. Material and Methods: Thirty adult male albino rats weighing between 200-250 grams were used in the present study. The animals were divided into three equal groups: Group I (control group), Group II (carbimazole induced hypothyroidism group): Rats received a daily dose of carbimazole (5mg/250g/day) for 5 weeks, Group III (BM-MSCs treated group): Hypothyroidism was induced similar to group II, then rats were injected with 1x 107 BM-MSCs cells. All Rats were euthanized after 8 weeks (5 weeks of hypothyroidism induction + 3 weeks of stem cells injection). Results: group (II) showed excessive destruction and degenerative changes of the acini and ducts in comparison to group (I), while group (III) revealed marked improvement of the parenchymal elements after BM-MSCs injection. Conclusions: This study supposes that BM-MSCs improve salivary glands damage following induction of hypothyroidism. Therefore, BM-MSCs can be applied as cell-based therapy for restoration of hypothyroid-induced salivary hypofunction.