The present review is concerned with the role of different physiological systems (e.g., skin conductance, heart rate, electromyography, and the eye-bling startle reflex) in understanding heterogeneity in conduct disorder (CD). Four subtyping approaches are considered: age of onset, comorbid psychopathology, callous-unemotional traits, and proactive/reactive aggression. Empirical findings are discussed in terms of distinct theoretical perspectives that aim to explain CD behaviors based on physiological over-arousal, under-arousal, and empathy deficits. According to the studies reviewed, the callous-unemotional (CD + CU) and internalizing (CD + Internalizing) sub-types can best inform CD heterogeneity. Findings indicated that children in the CD + CU and CD + Internalizing subtypes score on opposite extremes on heart rate, skin conductance and startle reactivity measures. Heart rate variability and respiratory sinus arrhythmia dysfunctions, associated with emotional dysregulation, were more evident among children in the CD + Internalizing group, while dysfunctional facial electromyography activity, which has been linked with reduced empathy, with the CD + CU group. In conclusion, it might be important to redefine CD diagnostic criteria based on physiological heterogeneity to enable the identification of distinct subtypes of CD.