Congenital chloride diarrhea (CCD) is a rare autosomal recessive disease. It is caused by mutations in the SLC26A3 gene which encodes the transmembrane Cl-/HCO3- exchanger, mainly expressed in the apical epithelium of the ileum and colon. The result is defective intestinal absorption of Cl- and secretion of HCO3-, leading to watery Cl- -rich diarrhea. The first symptoms of CCD include polyhydramnios and dilated intestinal loops of the fetus and they are followed by watery diarrhea, recurrent vomiting, failure to thrive, hypochloremic alkalosis, hypokalemia and hyponatremia in postnatal life. We present the case of an 8-year-old girl with late diagnosis of CCD, initially treated as Bartter syndrome. The incorrect diagnosis resulted from the clinical and biochemical similarities of both these disorders. Finally, CCD was confirmed by a genetic test, which revealed mutation in the SLC26A3 gene (p.IIe(TCA)657dup). Specific therapy led to alleviation of the CCD consequences and ensured normal physical and psychological development of the child. The case shows the difficulties in differential diagnosis between CCD and Bartter syndrome and indicates the benefits of molecular evaluation.