Abstract: Most accounts of the Enneagram describe relationships between each of the three major triads and the negative emotions of fear, anger, and sadness or social distress. This paper explores those relationships from a perspective that draws on contemporary scientific thinking in the fields of neurobiology, emotion, emotion regulation, and evolutionary biology. The hypothesis is that the structure of each of the nine Enneagram types is built around a particular pattern of emotion regulation relating to innate mammalian emotion systems governing fear, anger, and social distress. These patterns emerge in early life as cognitive-emotional structures which reside in neural networks responsible for emotion generation and its regulation. From a neurobiological perspective, we are born with a brain that has innate emotional capacities and temperamental tendencies. However, these tendencies must be “tuned” to and by actual life experience to create reasonably stable and socially functional emotion systems. One manifestation of these cognitive-emotional structures is Enneagram type. The bad news is that Enneagram emotional and mental “habits” are rooted in primal emotion systems. The good news is that these systems remain teachable throughout life, and that neurobiology provides insight into the processes of growth that take place as we begin to work seriously with our type. From a scientific perspective, it may be that the characteristics of each Enneagram type represent a fundamental skill set required for navigating human inner emotional terrain. It may also be the case that the variety of different types has been central to the evolutionary success of our innately social species.