The principles of hierarchical organization and progressive increase of differentiation and integration within a hierarchy provide a framework for understanding how the subjective experience of emotion, brain mechanisms mediating emotion and autonomic activation during emotional arousal are organized, and how the three domains are interrelated. Supporting evidence from empirical studies of three types, pairing one domain with each of the other two, are reviewed. This integrated model may bring coherence to the study of emotion, and facilitate an improved understanding of the role of emotion in systemic medical disorders.