Background: Stem cells are one of the most fascinating areas of biology today they play an important role in our bodies from embryonic development through adulthood, and diabetes mellitus (DM) is one of the most common degenerative diseases that affect all body tissues and organs. Objectives: The aim of this study was to evaluate the effect of bone marrow derived stem cells on the submandibular salivary glands in diabetic rats. Materials and methods A Total of sixty, adult male albino rats with body weight ranging from 180-200 grams were used in the present investigation. They were divided as follows, Group 1 (15 animals) served as controls. Group 2 (15 animals), they were subjected to a single intraperitoneal injection of streptozotocin. Group 3: consisted of 30 animals, they were subdivided as follows: Subgroup 3.1 (15 animals), they were used for isolation and culture of bone marrow stem cells and Subgroup 3.2: (15 animals)they were subjected to a single intraperitoneal injection of streptozotocin, the same as group 2, in a dose of 60 mg/kg body weight for induction of diabetes mellitus. One week later, they were subjected to a single intravenous infusion of mesenchymal bone marrow stem cells. At the end of the experiment the animals of the different groups were sacrificed by cervical dislocation, their submandibular salivary glands dissected out, separated into right and left glands for histological and ultrastructural examination. Results Light and transmission electron microscopic results showed the degenerative changes of diabetes in group 2 and the high regenerative changes of bone marrow derived stem cells in group 3.2 compared to the control group 1. Conclusion Stem cells have magnificent regenerative effect in diseased and injured tissues in different organs.