Human and animal research has long documented the negative effects of early traumatic events on long-term development and socioemotional behavior. Yet, how and where the body stores these memories remains unclear. Current theories propose that the brain stores such memory in the subcortical limbic system. However, a clear theory of change with testable hypothesis has yet to emerge.In this paper, we review the classical Pavlovian conditioning learning tradition, along with its functional variant. Then, we review calming cycle theory, which builds upon the idea that mother/infant learning is distinct from other types of learning, requiring a new set of assumptions in light of functional Pavlovian conditioning.Calming cycle theory states that learning of behaviors associated with subcortical autonomic physiology is separate and distinct from learning of behaviors associated with cortical physiology. Mother/infant autonomic learning starts in the uterine environment via functional Pavlovian co-conditioning that is stored as conditional reflexes within the dyad's autonomic nervous systems. These reflexes are preserved transnatally as autonomic socioemotional reflexes (ASRs), which can be used to monitor mother-infant relational health. The functional Pavlovian co-conditioning mechanism can be exploited to change the physiological/behavioral reflex response. The theory provides a well established learning mechanism, a theory of change and a method of change, along with a set of hypotheses with which to test the theory. We present evidence from a randomized controlled trial with prematurely born infants and their mothers that supports calming cycle theory.