Background and aims Mitochondrial swelling is involved in the pathogenesis of many human diseases associated with oxidative stress including obesity. One of the strategies for prevention of deleterious effects related to obesity and overweight is engaging in regular physical activity, of which high intensity interval training (HIIT) is efficient in promoting biogenesis and improving the function of mitochondria. Therefore, our aims were to investigate the effects of HIIT on metabolic and neuro-cardiovascular dynamic control and mitochondrial swelling induced by high-fat diet (HFD). Methods and results Twenty-three male Wistar rats (60 – 80g) were divided into 4 subgroups: control (C), HIIT, HFD and HFD+HIIT. The whole experimentation period lasted for 22 weeks and HIIT sessions were performed 5 days a week during the last 4 weeks. At the end of the experiments, fasting glucose and insulin tolerance tests were performed. Cerebral microcirculation was analyzed using cortical intravital microscopy for capillary diameter and functional density. Cardiac function and ergoespirometric parameters were also investigated. Mitochondrial swelling was evaluated on brain and heart extracts. HFD promoted an increase on body adiposity (p<0.001), fasting glucose levels (p<0.001), insulin resistance index (p<0.05), cardiac hypertrophy index (p<0.05) and diastolic blood pressure (p<0.05), along with worsened cardiac function (p<0.05), reduced functional cerebral capillary density (p<0.05) and its diameter (p<0.01), and heart and brain mitochondrial function (p<0.001). HFD did not affect any ergoespirometric parameter. After 4 weeks of training, HIIT was able to improve cardiac hypertrophy index, diastolic blood pressure, cerebral functional capillary density (p<0.01) and heart and brain mitochondrial swelling (p<0.001). Conclusion In animals subjected to HFD, HIIT ameliorated both cerebral mitochondrial swelling and functional capillary density, but it did not improve cardiovascular function suggesting that the cardiovascular dysfunction elicited by HFD was not due to heart mitochondrial swelling.