Early diagnosis of diarrhea is critical to prevent disease progression. Diarrhea in newborns can be congenital or acquired; acquired diarrheas are the major cause in infants. Congenital diarrheal diseases are rare and include defects in digestion, absorption, and transport of nutrients, and electrolytes; disorders of enterocyte differentiation and polarization; defects of enteroendocrine cell differentiation; dysregulation of the intestinal immune response; and dysfunction of the immune system. This review discusses the clinical approach that may help in early identification and management of different congenital diarrheal diseases.