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Cystinuria is an autosomal recessive disorder of the kidneys and small intestine, affecting a luminal transport mechanism shared by cystine, ornithine, arginine and lysine. When cystine exceeds its solubility at low pH, the risk of stone formation increases. The data reported in the literature show a variation for the incidence of cystinuria, from 1 in 600 to 1 in 17,000, depending on the definition of cystinuria and the method used for screening the population. We set up a pilot screening programme to determine the incidence of cystinuria in the population of the Valencian Community. Urine filter paper samples submitted for the neonatal screening programme from 33,995 newborns (5–10 days old) were used for the study. Thin layer chromatography (TLC) was performed to screen cystinuric patients. To confirm positive filter paper samples, liquid samples were requested and TLC as well as the cyanide-nitroprusside test (CNT) were performed. Final diagnosis was achieved by quantifying cystine, lysine, ornithine and arginine using high-performance liquid chromatography (HPLC) in children's urine samples which remained positive for TLC and CNT for more than 1 year. We conclude that the incidence of subjects at risk for cystine stones in the Valencian Community is 1:1887. TLC is shown as a reliable method to perform newborn screening in large population to detect cystinuric subjects. Additional studies, including characterization of appropriate haplotypes, should be carried out for a more precise identification of the frequency of the different types of cystinuria in our population.