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Unmanaged emotional reactions to stress not only lead to behavior problems in young people but also create physiological conditions that inhibit learning and potentially increase the risk of disease later in life. For these reasons, the integration of emotional self-management skills training programs has become an increased priority in some schools. In this study, middle school students enrolled in a course in emotional competence skills learned techniques designed to intercept stressful responses during emotionally challenging situations. Behavioral outcomes were assessed using the Achievement Inventory Measure and autonomic function was measured by heart rate variability (HRV) analysis during and after a stressful interview. Following the program, students exhibited significant improvements in areas including stress and anger management, risky behavior, work management and focus, and relationships with family, peers and teachers. These improvements were sustained over the following six months. Students using the skills taught in the course to recover from acute emotional stress were also able to positively modulate their physiological stress responses. As compared to a control group, trained students demonstrated significantly increased HRV and more rhythmic, sine wave-like heart rhythm patterns during recovery. This response pattern reflects increased parasympathetic activity, heart rhythm coherence and entrainment of other biological oscillatory systems to the primary heart rhythm frequency. Increased physiological coherence is associated with improved cognitive performance, emotional balance, mental clarity and health outcomes. These physiological shifts could promote the sustained psychological and behavioral improvements associated with the use of emotional management skills. It is suggested that learning emotional competence skills in childhood establishes healthier physiological response patterns which can benefit learning and long-term health. Results provide support for the integration in school curricula of courses designed to teach effective self-management skills to children.