Abstract: Objective　To explore the clinical features and genetic etiology of children with cystinuria with onset of kidney stone. Methods　The clinical data of 3 children with cystinuria with onset of kidney stone and the gene analysis results of SLC3A1 and SLC7A9 by PCR sequencing were retrospectively analyzed. Results　Three male children were from three unrelated families, kidney stone were presented in 2 cases at 1 year old and 1 case at 14 years old. The blood amino acid spectrum was normal in all 3 cases, while the free carnitine were decreased. The urinary amino acid spectrum indicated that cystine, ornithine, arginine, and threonine increased. Gene analysis confirmed that 1 case had homozygous mutations of SLC7A9 gene c.325G>A, and his parents were carriers of c.325G>A heterozygous mutation; other 2 cases had heterozygous mutations of SLC3A1 gene, c.1365delG and c.1113C>A heterozygous mutation in one case, and c.1897_1898insTA and c.1093C>T heterozygous mutation in one case, and their parents were heterozygous mutation carriers. After treatment with potassium citrate and L-carnitine, the conditions were improved in all cases. Conclusions　Inherited metabolic disease should be considered for children with kidney stone. Urine amino acid analysis and gene detection are important methods for the diagnosis of cystinuria.