Maternal‐neonate separation for human newborns has been the standard of care since the last century; low birth weight and preterm infants are still routinely separated from their mothers. With advanced technology, survival is good, but long‐term developmental outcomes are very poor for these especially vulnerable newborns. The poor outcomes are similar to those described for adversity in childhood, ascribed to toxic stress. Toxic stress is defined as the absence of the buffering protection of adult support. Parental absence has been strictly enforced in neonatal care units for many reasons and could lead to toxic stress. The understanding of toxic stress comes from discoveries about our genome and epigenetics, the microbiome, developmental neuroscience and the brain connectome, and life history theory. The common factor is the early environment that gives (a) signals to epigenes, (b) sensory inputs to neural circuits, and (c) experiences for reproductive fitness. For human newborns that environment is direct skin‐to‐skin contact from birth. Highly conserved neuroendocrine behaviors determined by environment are described in this review. The scientific rationale underlying skin‐to‐skin contact is presented: autonomic development and regulation of the physiology leads to emotional connection and achieving resilience. Maternal‐neonate separation prevents these critical neural processes from taking place, but also channel development into an alternative developmental strategy. This enables better coping in a stressful environment in the short term, but with permanently elevated stress systems that negatively impact mental and physical health in the long term. This may explain the increasing incidence of developmental problems in childhood, and also Developmental Origins of Health and Disease. Arguments are presented that maternal‐neonate separation is indeed a source of toxic stress, and some suggestions are offered toward a “zero separation” paradigm.