Objective To explore the effect of melatonin on mitochondria in streptozotocin (STZ)-induced diabetic rats and its potential mechanism. Methods The diabetic rat models were induced by intraperitoneal injection of STZ, and the diabetic rats were randomly divided into two groups: diabetes mellitus group (DM group) and melatonin-treated group (DM± MT group). The normal non-diabetic rats were served as control group. Mitochondrial membrane potential and mitochondrial swelling were measured, the expression of voltage-dependent anion channel (VDAC)was assayed by immunohistochemistry in the heart, liver and kidney among the different groups after 8 weeks. Results (1)Compared with DM group, mitochondrial membrane potential in the heart,liver and kidney were significantly elevated in DM± MT group (553.6± 193.5 vs. 311.4 ± 133.7;745.7±115.8 vs. 358.9±158.7; 951.6±246.1 vs. 425.8±177.9, all P＜0.05). (2)Compared with DM group, mitochondrial swelling in the heart, liver and kidney was reinforced in DM ± MT group. (3)Compared with DM group, the expressions of VDAC in the heart, liver and kidney were significantly up-regulated in DM± MT group (76.93 ± 8.263 vs. 58.59 ± 7.62, 50.69 ± 6.33 vs.40.11±6.30, 77.86±8.59 vs. 61.44± 12.86, all P＜0.05). Conclusions Melatonin has protective effect on the activity of mitochondria in the heart, liver and kidney in diabetic rats possibly by up-regulating the expression of VDAC.