Objective　Familial hypomagnesemia with hypercalciuria and nephrocalcinosis (FHHNC) is an autosomal recessive genetic disease caused by CLDN16 or CLDN19 gene mutation. This paper is aimed to discuss the clinical characteristics and disease—causing mutations in FHHNC. Methods　Clinical data of a patient with FHHNC was retrospectively analyzed. Results　A two months old patient with hypomagnesemia and nephrocalcinosis in bilateral kidneys was admitted. The child had low blood magnesium and high urinary calcium; renal ultrasound indicated enhanced renal medullary echo, with repeated positive results of the urine cultures of Escherichia coli. Gene sequencing showed two heterozygous variants c.324+1G>C, c.317C>T in the CLDN16 gene (p.Ser106Phe). It was clinically improved after being treated orally with anti-infection and 25% magnesium sulfate, potassium magnesium aspartate, and 10% sodium citrate. Conclusion　FHHNC is a rare disease with poor prognosis. At present, there is no special treatment except transplantation. Gene testing is helpful for early diagnosis of FHHNC.