Objective　To discuss the clinical diagnosis, treatment and genetic diagnosis of congenital chloride diarrhea (CCD), a rare autosomal recessive disease. Methods One month old boy with persistent diarrhea, hypochloremia, hyponatremia, hypokalemia and metabolic alkalosis, his stool electrolyte testing, clinical treatment and follow-up, as well as his and his parents’ SLC26A3 gene mutation analysis were retrospectively analyzed. Results The fecal electrolyte testing showed that the levels of Cl- and K+ were increased and the level of Cl- was much higher than the sum of Na+ and K+. After replacement therapy with NaCl and KCl, the blood electrolyte recovered to normal. Follow-up 4 years, the boy had a normal growth and development. Mutation analysis on SLC26A3 gene showed there was a homozygous mutation of 239G>A and both his father and mother carried the same heterozygous mutation. This mutation was first discovered in China. Conclusions The sequencing analysis of SLC26A3 mutation may help to diagnosis CCD.