Introduction: Brain-Behavioral Systems contribute to the development of wide variety of emotional disorders, including anxiety and depression. The aim of this study was to compare the Brain-Behavioral Systems in patients with anxiety, patients with depression, and healthy individuals. Materials and Methods: This study was a cross-sectional study in which 45 individuals with anxiety (moderate to high score in Beck Anxiety Inventory (BAI) and low score in BDI-II) and 45 individuals with depression (moderate to high score in Beck Depression Inventory-II (BDI-II) and low score in BAI) who referred to private and public health centers in Jiroft were selected through purposive sampling and matched with 45 healthy individuals (low score in BDI-II and BAI) for age and gender. After informed consent, participants were asked to fill the questionnaires including Jackson-5 Scale, 2nd version of Beck Depression Inventory (BDI-II), and Beck Anxiety Inventory (BAI) and were allocated to different groups based on the score of the questionnaires. Data were analyzed using one-way analysis of variance by spss21 software. Results: Result showed that there were significant differences between three groups in Behavior Inhibition System, Fight, Flight and Freeze. Also, the differences were not significant in Behavioral Activation System. Conclusion: Given the different functions of the Brain-Behavioral Systems in patients with anxiety, patients with depression, and healthy individuals, this theory may explain the etiology of anxiety and depression.