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Background: Diabetes mellitus is a widespread disease disrupting cognitive function. We investigated the effect of eight-week high-intensity interval training (HIIT) and caffeine supplementation on Brain-derived neurotrophic factor (BDNF) and glial line-derived neurotrophic factor (GDNF) in a rat diabetic model. Methods: In this experimental study, streptozotocin-induced diabetic rats were randomly divided into: control (C), diabetic (D), diabetic+caffeine (D+CA), diabetic+training (D+T) and diabetic+training+caffeine (D+T+CA) groups. Training groups underwent a high-intensity interval training program (5 sessions a week over 8 weeks). The supplement groups were administered with 7mg caffeine/100gr body weight for 5 days a week before each exercise session throughout the experimental period. The rat hippocampus and brainstem were removed 48 h after the last training session and blood samples were taken from left ventricle. The levels of glucose, BDNF and GDNF were measured by ELISA assay. Data were analyzed using two-way ANOVA test. Results: Streptozotocin-induced diabetes increased blood glucose (p <0.01) whereas decreased BDNF and GDNF levels (P=0.002). The results showed that HIIT decreased blood glucose (P=0.002) but increased BDNF and GDNF levels in diabetic rats (P=0.003 and P=0.001, respectively). Even though caffeine supplementation significantly reduced blood glucose concentration (P=0.0001), it had no significant effect on BDNF and GDNF levels in diabetic rats (P>0.05). We also observed a significant interaction between treatments regarding GDNF changes (P=0.024); yet, the interaction between caffeine and HIIT on BDNF did not reach the significance level (P=0.074). Conclusion: Based on the findings, HIIT increased BDNF and GDNF levels in rat diabetic model, but caffeine ingestion had no significant effect on neurotrophic factors. However, caffeine seems to blunt HIIT-induced increase in neurotrophic factors which remains to be further investigated.