Neonatal stress is a common early life event which alters the development of the endocrine and immune systems. Specifically, exposure to neonatal stress results in alterations to the hypothalamic–pituitary–adrenal (HPA) axis resulting in offspring who hyper-respond to stress in adulthood. Recently, this concept has been applied to the ontogeny of functional gastrointestinal (GI) disturbances such as irritable bowel syndrome (IBS). The high prevalence of this disorder and the ineffectiveness of current treatments results in high direct and indirect costs to the society. Recently, administration of probiotics to neonates has been used as a safe and cost-effective preventative strategy to revoke the long term unfavourable imprinting induced on the gastrointestinal system by early life stressors in animal models of human IBS. It is not as yet known however, whether maternal supplementary probiotics may also contribute to improved GI integrity and gut-associated immune functioning in stressed neonates, if these possible improvements persist into adulthood, or how this protective effect may be mediated. Our hypothesis is an attempt to link this proposed nutritional approach and its possible preventive effects against GI dysfunctions provoked by neonatal stress.