There is growing evidence for the involvement of the gut-microbiota in the regulation of emotions, behavior, and higher cognitive functions through the 'microbiome-gut-brain axis'. This relationship between the gut microbiota and the brain is pivotal for the development of the newborn, which receives its commensal microbiota at birth; dysbiosis may result in altered neurodevelopment. The hypothalamus-pituitary-adrenocortical (HPA) axis is actively involved in the stress response but is undeveloped in the newborn. Here, we describe how changes in the commensal microbiota influence the normal development of the HPA axis and review recent findings describing the essential crosstalk between the gut microbiota and the HPA axis and suggesting a role for the maternal and commensal microbiota in the development of the HPA axis and of the stress response.