Background: To clarify the distinction between anxiety and depression, the tripartite model was introduced. According to this model, physiological hyperarousal (PH, i.e. autonomic hyperactivity) is specific for anxiety and not depression. Research on the relation between anxiety, depression and physiological measures representing arousal is lacking. Methods: Parent-and self-reported anxiety and depressive problems were assessed using the CBCL and RCADS. Heart rate (HR), heart rate variability in the low frequency (HRV LF) and respiratory sinus arrythmia (RSA) were used as indices for autonomic arousal. Results: Parent-reported anxiety was associated with low RSA in supine posture. This association was also found for self-reported anxiety problems, but only in boys. These findings point towards high arousal in anxiety. Self-reported depressive problems were associated with low HRV LF in standing posture and high RSA in supine posture in boys, pointing towards low arousal in depression. However, self-reported depressive problems were also associated with high HR in standing posture and with low HRV LF in supine posture in girls, suggesting high arousal in depression. Limitations: Although HRV LF in standing posture is primarily sympathetically mediated, and HRV LF in supine posture is primarily vagally mediated, the association between HRV LF and sympathetic versus vagal function is not exclusive. Thus, HRV LF measures are merely approaches of high or low arousal. Conclusions: Some evidence was found for hyperarousal in anxiety, but also for hyperarousal in depression. Apparently, the idea of hyperarousal in anxiety and not in depression is too simple to reflect the more complex reality.