Cystinuria is a hereditary disorder caused by a defect in the apical membrane transport system for cystine and dibasic amino acids in renal proximal tubules and intestine, resulting in recurrent urolithiasis. Mutations in SLC3A1 and SLC7A9 genes, that codify for rBAT/b^0,+AT transporter subunits cause type A and B cystinuria respectively. In humans, cystinuria treatment is based on the prevention of calculi formation and its dissolution or breakage. Persistent calculi are treated with thiols (i.e., D-penicillamine (DP) and mercaptopropionylglycine (MPG)) for cystine solubilisation. We have developed a new protocol with D-penicillamine to validate our Slc7a9 knockout mouse model for the study of the therapeutic effect of drugs in the treatment of cystine lithiasis. We performed a 5-week treatment of individually caged lithiasic mutant mice with a previously tested D-penicillamine dose. To appraise the evolution of lithiasis throughout the treatment a non-invasive indirect method of calculi quantification was developed: calculi mass was quantified by densitometry of X-ray images from cystinuric mice before and after treatment. Urine was collected in metabolic cage experiments to quantify amino acids in DP-treated and non-treated non-lithiasic mutant mice. We found significant differences between DP-treated and non-treated knockout mice in calculi size and in urinary cystine excretion. Histopathological analysis showed that globally non-treated mutant mice had more severe and diffuse urinary system damage than DP-treated mice. Our results validate the use of this mouse model for testing the efficacy of potential new drugs against cystinuria.