Early childhood education programs, and particularly those designed to reduce gaps in school readiness between children in poverty and their more affluent peers, have increasingly addressed children's self-regulatory abilities -- their ability to manage behaviors, emotions, and cognitive processes. Although self-regulation is typically defined in volitional terms, the activity of multiple, involuntary, neurophysiological systems scaffolds the development of effortful self-regulation. In this article, we argue that the activity of one of these neurophysiological systems, the parasympathetic nervous system (PNS), is directly relevant to the design and evaluation of early childhood education programs, given that the PNS makes moment-to-moment adjustments in children's metabolic output to support their interaction with the classroom environment. We go on to explain how examining PNS activity while children are in the early education classroom may offer insight into how early education programs achieve their effects and for whom these effects are most-fully realized. We conclude by offering a summary of modern methods of parasympathetic data collection and cleaning drawn from a recent study of young children in an early education environment and discussing the implications of these methods for future research.