Studies of enteric diseases have historically focused on observations of clinical diarrhea as a cause of mortality and morbidity. Emerging evidence suggests that diarrhea dramatically underestimates both exposure to enteropathogens and the long-term consequences arising from infection. High burden of pathogens in the gut, even in the absence of diarrhea, is common in infants in low and middle income countries. Continual challenge by pathogens, in conjunction with an inadequate diet stimulates an inflammatory disease that alters the structure of the gut, metabolic and immunological pathways and changes the microbiome. Both diarrhea and enteropathogen infection have been associated with reduced growth, reduced cognitive development, and reduced vaccine efficacy suggesting that the burden of diarrheal disease is dramatically underestimated.