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Heart rate variability (HRV) is a measure of the beat-to-beat variations in heart rate related to the work of autonomic nervous system. It may serve as a psychophysiological indicator for arousal, emotional state and stress level. We used this parameter in both the assessment and biofeedback training, for dealing with five groups of common mental health problem in school children (anxious-phobic, somatoform, obsessive-compulsive, attention deficit hyperactivity and conduct disorders). The obtained results were compared with healthy children at the same age. In order to define the four main characteristics of personality (extroversion/introversion, neuroticism/ stability, psychopathological traits and honesty) Eysenck Personality Questionnaire was applied. Results showed significantly higher psychopathological traits in ADHD and somatoform group, lower extroversion in somatoform, higher neurotism in OCD and lower lie scores in ADHD and OCD groups. As HRV instrument we used Heart Math Freeze-Framer System. After 15 sessions of training, children from nearby all groups showed improved high and medium HRV which corresponded to the improved clinical outcome. Hereby, the best results were obtained for conduct and anxiety disorder, and the worst for ADHD.