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Anorexia Nervosa (AN) is associated with a high rate of morbidity and mortality as well as a high rate of relapse. The molecular mechanisms underlying the progression of the disorder or the relapses are largely unknown. Patients with AN have been shown to have increased oxidative stress, but its involvement in the development in the disease is unknown. We have previously shown that adolescent female rats undergoing the activity-based anorexia (ABA) paradigm also show signs of oxidative stress. Due to their role in the release of reactive oxygen species (ROS), mitochondria are of high interest in diseases exhibiting oxidative stress. In this study, the impact of ABA on brain mitochondrial dynamics was examined. We found transient changes in the medial prefrontal cortex, hypothalamus, and hippocampus following 25% weight loss and changes in the amygdala at a 10-day weight recovery timepoint. These changes point towards damage in the mitochondria contributing to the oxidative stress.