Cystine stones belong to the kidney stones diseases which are difficult to manage due to the high rate of recidivation and the necessary surgical procedures. Cystinuria is an autosomal recessive defect of the transport of cystine and the dibasic amino acids in the proximal kidney tube. Recently, two subunits of a renal cystine transporter have been identified. Mutations in these genes have been shown to lead to the cystinuria phenotype. Genetic and functional analyses have helped to modify the classification of cystinuria which had previously been exclusively based on biochemical data. Furthermore, first steps towards a molecular genetic testing have been carried out replacing the so far diagnostic procedure which are stressing for the patients. The results of these testings make an individual therapy possible.