It is often reported that children with oppositional deviant disorder (ODD) or conduct disorder (CD) are under-aroused. However, the evidence is mixed, with some children with ODD/CD displaying high arousal. This has led to the hypothesis that different profiles of arousal dysfunction may exist within children with ODD/CD. This knowledge could explain variability within children with ODD/CD, both in terms of specific types of aggression as well as comorbid symptoms (e.g., other emotional/behavioral problems). We measured heart rate variability (HRV), heart rate (HR) and skin conductance level (SCL) during rest and stress, and obtained parent and teacher reports of aggression, anxiety, attention problems and autism traits in a sample of 66 ODD/CD and 36 non-clinical boys (aged 8-12 years). The ODD/CD group scored significantly higher on aggression, anxiety, attention problems and autism traits than the controls; boys with ODD/CD also had higher resting HRs than controls, but HR stress, HRV and SCL did not differ. Hierarchical regressions showed different physiological profiles in subgroups of boys with ODD/CD based on their type of aggression; a pattern of high baseline HR and SCL, but low stress HRV was related to reactive aggression, whereas the opposite physiological pattern (low HR, low stress SCL, high stress HRV) was related to proactive aggression. Furthermore, high stress SCL was related to anxiety symptoms, whereas low stress SCL was related to attention problems. These findings are important because they indicate heterogeneity within boys with ODD/CD and highlight the importance of using physiology to differentiate boys with different ODD/CD subtypes.