The aim of this study has been to know the prevalence of the four most common mutations reported in SLC3A1 gene involved in human cystinuria, and to estimate the association with different phenotypic manifestations of this disease in population of the Valencian Community, Spain.We have carried out a cross-sectional study with a control group in 16 families with one or more members diagnosed as cystinuric patients. 149 subjects (38 cystinuric patients, 39 relatives and 72 controls) were studied. Genetic analyses were carried out using PCR (polymerase chain reaction), RFLPs (restriction fragment length polymorphisms) and sequencing of PCR products. Parametric and non parametric tests were applied in the statistical analyses.None of the four mutations studied were found in the control group. M467T mutation was the most prevalent in cystinuric patients as well as in relatives, showing and allelic frequency of 0.06 and 0.03 respectively. Regarding to the association analysis between genotype and phenotype, we found that, in cystinuric subjects, urinary excretion of some dibasic amino acid was higher in those who carried M467T mutation (p < 0.05). The formation of cystine crystals was also higher in cystinuric patients who carried this mutation (p < 0.05).Prevalences of recurrent mutations reported up to now in SLC3A1 gene are very low in cystinuric subjects of the Valencian Community, Spain. Only mutation M467T has been found, without differences between cystinuric and their relatives, although in the first ones was associated with a more accurate phenotype manifestation of the disease.