Using exome sequencing analysis of a panel of genes associated with nephrolithiasis and nephrocalcinosis, we have identified a novel homozygous missense mutation, c.1361C>T; p.(T454M) located in the SLC34A1 gene and a previously described heterozygous 101 bp deletion in the SLC34A3 gene of a six-month-old girl with failure to thrive, polyuria, nephrocalcinosis, hypercalcemia, phosphate levels in the lower limit and elevated levels of 1,25-(OH)2D3. Here, SLC34A3 is linked to nephrolithiasis.