What causes cystine stones?

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Cystine stones form when there is a genetic defect in the kidney’s ability to reabsorb certain amino acids, especially cystine. This condition, cystinuria, causes excess cystine to spill into the urine. Cystine has relatively low solubility in urine, so when it is present in high concentrations it tends to precipitate and form stones. Because the underlying issue is the impaired reabsorption of cystine (and related dibasic amino acids), the stones arise specifically from too much cystine in the urine, not from excess calcium or oxalate, and not from very acidic urine alone.

In contrast, excessive calcium in urine points to calcium stones, and excessive oxalate (hyperoxaluria) also favors calcium-based stones. Urine that is very acidic (pH below 5) predisposes to uric acid stones, not cystine stones. Keeping urine more alkaline can help dissolve or prevent cystine crystals, which aligns with the mechanism of cystinuria.