Case report: A 8 year-old-male patient born of consanguineous marriage was diagnosed as lysinuric protein intolerance by hypotonia, feeding problems and urine amino acid analysis at the age of 2 months and protein restriction and L-citrulline therapy was started. The patient was reevaluated when 8 years old because of the absence of hyperammonemia attacks even on a high protein intake, normal blood ferritin, lactate dehydrogenase levels and hypotonia-cystinuria syndrome was suspected. There was no sign of nephrolithiasis or urolithiasis. The plasma and urine amino acid analysis revealed normal plasma and high urine levels of lysine, arginine, ornithine, cystine. The demonstration of a homozygous deletion in SLC3A1 and PREPL genes confirmed the the diagnosis of HCS.