Undernutrition contributes to more than 40% of the global child mortality rate. In 2014 stunting, which is the main manifestation of chronic undernutrition, affected 159 million children. Stunting entails long-term repercussions for the child, such as impaired growth, defective immune response, and neuro-cognitive consequences. Epidemiologic studies emphasize that undernutrition cannot be ascribed solely to food insecurity and that early life environmental exposures play a major role in the pathogenesis of the disease. Indeed, growing evidence indicates that a syndrome called pediatric environmental enteropathy (PEE) undermines the physiological nutrition process. PEE is a chronic low-grade inflammation of the small intestine in response to repeated exposure to a highly microbiologically contaminated environment. This entails changes in the resident gut microbiota and intestinal atrophy, eventually leading to nutrient malabsorption, and deficient responses to live-oral vaccines. Estimates indicate that up to 75-100% of children living in the most impoverished areas with high prevalence of enteric infections suffer from PEE. Identifying how the infant acquires a pediatric environmental enteropathy and a dysbiotic gut microbiota are the crucial questions to elucidate the pathological pathways associated with malnutrition and design future intervention strategies.