Cystinuria is an autosomal recessive disease caused by mutations in SLC3A1 (rBAT) and SLC7A9 (b^0,+AT). Gene targeting of the catalytic subunit (Slc7a9) in mice leads to excessive excretion of cystine, lysine, arginine and ornithine. Here we studied this non-type I cystinuria mouse model using gene expression analysis, Western blot, clearance and uptake experiments to characterize the renal and intestinal consequences of losing Slc7a9 function. The electrogenic and flux transport studies in the intestine suggested that arginine and ornithine are transported via other routes apart from system b^0,+. No remarkable gene expression changes were observed in other amino acid transporters and the peptide transporters in intestine and kidney. Further, the glomerular filtration rate (GFR) was reduced by 30 % in knockout animals compared to wild-type animals. The fractional excretion of arginine was increased as expected (~100 %), but fractional excretions of lysine (~35 %), ornithine (~16 %) and cystine (~11 %) were less affected. Loss of function of b0,+AT reduced transport of cystine and arginine in renal brush border membrane vesicles and completely abolished the exchanger activity of dibasic amino acids with neutral amino acids. In conclusion, loss of Slc7a9 function decreases the glomerular filtration rate and increases the excretion of several amino acids to a lesser extent than expected with no clear regulation at the mRNA and protein level of alternative transporters and no increased renal epithelial uptake. These observations indicate that transporters located in distal segments of the kidney and/or metabolic pathways may partially compensate Slc7a9 loss of function.