Cystinosis and cystinuria, both recessive genetic disorders, are fundamentally different in their pathophysiologic mechanisms. Cystinosis is a disease of cystine storage in which the kidney is the initial, but not the sole target organ. Cystinuria is a disease of renal tubular cystine transport in which excessive loss of this insoluble amino acid causes precipitation at physiologic urine pH and concentration. The former disorder uniformly results in the need for renal allograft despite recent advances in medical therapy. Cystinuria has a variable severity of expression and may be amenable to long-term medical treatment in some patients. Others may have frequent stone recurrence and infection and progress to chronic renal failure in the long term. It is the purpose of this review to provide the reader with an understanding of the respective diseases and the reasons for the differences in their prognoses and long-term outcomes.