In children, diarrhea has a global incidence of 2.7 episodes per child-year and contributes to significant disease burden and mortality in children under 5 years of age. Chronic diarrhea, defined as diarrhea lasting for more than 2 weeks, may be particularly challenging to evaluate and manage in children under 2 years of age. While most have infectious enteritis or cow milk protein intolerance, others have conditions such as malnutrition, anatomic abnormalities, or congenital enteropathies that can be challenging to diagnose and treat. We present here a complex case of chronic diarrhea in an infant and highlight such diagnostic and therapeutic challenges.