In the developing world major public health issues such as malnutrition and compromised physical development are intimately linked to altered gut morphology and function with underlying chronic inflammatory responses. In these societies the downward spiral of malnutrition and infections does not seem to be remedied by well-informed nutritional interventions that supplement the identified nutrient deficiencies, suggesting that additional strategies are needed. The aim of this scientific opinion paper is to consider how a child from the developing world might benefit, separately and additively, from interventions targeted to impact hygiene, nutritional status, disease resistance and gut function, if successful interventions could be found. A failure to tackle environmental enteropathy (EE) may be a critical limiting factor that can explain the relative lack of success of interventions focussed on micronutrient supplementation so far. Therefore this paper starts with a summary of the aetiology and consequences of EE on child health and the current recommendations aimed at tackling this problem. Then a number of hypotheses will be considered in terms of research strategy to positively affect nutritional status, intestinal health and growth of children with EE, with the aim of inspiring future innovative strategies, for both the food industry and the public health sector, which could benefit millions of children.