Cystinuria is an inherited disorder that causes kidney and urinary tract stones in dog, man and other animals and has been documented in over 60 breeds of dogs. In humans, mutations in the protein-coding regions of two genes (named SLC3A1 and SLC7A9) are found in affected individuals. In some dog breeds, cystinuria is an autosomal recessive trait caused by mutations in the SLC3A1 gene. However, in many dog breeds, the genetic basis of cystinuria is much more complex. We recently obtained data suggesting that: 1) that in at least one breed of dogs (Mastiffs), DNA changes near one of the “cystinuria genes” are associated with early cystine stone formation, and 2) that gender and reproductive status may affect the level cystine in the urine. Our most recent study has more precisely defined the region associated with early cystine stone formation in Mastiffs and analyzed DNA polymorphisms from the region in additional dogs. The data generated further supports the finding that polymorphisms near one of the cystinuria genes are associated with high risk of early stone formation. In summary, the studies indicate that it will be possible to develop a DNA-based test for breeders to use to reduce the incidence of particular (but not all) cystinuria predisposing alleles in the Mastiff population and to decrease the incidence of cystine stone formation in the Mastiff breed.