Background: Diabetes mellitus is a metabolic disease which affects the brain as well as other organs. Connection of mesencephalic raphe nuclei to striatum is important, and reduction of these projections can play a negative role in regulatory connection between them. Objectives: The main objective of this study was to determine the effects of diabetes on projections of mesencephalic raphe nuclei to striatum of rats. Materials and Methods: Forty eight male adult Wistar rats were divided into four groups (1.control, 2. two-month diabetic rats, 3. fourmonth diabetic rats and 4. six-month diabetic rats). HRP was injected into the dorsal and ventral striatum separately and after perfusion with normal saline, fixation, and postfix solutions, the brains were sectioned coronaly (40 µm). Frozen sections were reacted with TMB and counterstained with 1% neutral red. Results: This study showed reduction of labeled neurons in both mesencephalic raphe nuclei following induction of diabetes. After injection of HRP to ventral striatum this reduction was prominent in DR nucleus in comparison to median raphe projections to ventral striatum affected by diabetes more than that of those to dorsal striatum. Conclusions: Diabetes mellitus decreases the projections of mesencephalic raphe nuclei to striatum.