Cystinuria: An Inherited Cause of Repeated Kidney Stones


Cystinuria is an inherited condition in which the kidneys fail to take back an amino acid called cystine from the urine they are making. Cystine is very poorly soluble, so in people with cystinuria it builds up in the urine, forms crystals and then stones. A European clinical practice recommendation describes it as an autosomal recessive disorder in which high urinary cystine excretion leads to cystine stones "because of the low solubility of cystine at normal urinary pH" (Servais 2021). The stones tend to begin young and come back again and again, and the main question in the medical literature is how to stop the next one.

This page covers what goes wrong in the kidney, how common cystinuria is, how the stones form, how it is diagnosed, the treatments that guidelines and studies describe, the surgery used to remove stones, what happens to kidney function over the years, the newer agents being tested, and what is still not known. The general picture of kidney stones of every type is on the Kidney Stones page. Crystal damage of a different kind, from calcium oxalate settling inside the kidney tissue, is on the Oxalate Nephropathy page.


Table of Contents

  1. A Faulty Kidney Transporter
  2. Two Genes and Three Types
  3. How Common It Is
  4. How Cystine Stones Form
  5. When Stones Usually Begin
  6. How It Is Diagnosed
  7. Fluid and Urine Alkalinisation
  8. Salt and Protein in the Diet
  9. Thiol Drugs: Tiopronin and D-Penicillamine
  10. The Captopril Evidence
  11. Surgery to Remove Stones
  12. Kidney Function and Recurrence
  13. Newer Agents Under Study
  14. What Is Not Known
  15. Key Research Papers
  16. Connections
  17. Featured Videos

A Faulty Kidney Transporter

Every day the kidneys filter a large volume of fluid out of the blood. Most of the useful molecules in that fluid, including amino acids, are pulled back into the body by transporters in the first stretch of each kidney tubule, the proximal tubule. In cystinuria one of those transporters does not work. It normally carries cystine and three "dibasic" amino acids — lysine, arginine and ornithine — and the same transporter defect is found in the lining of the gut (Calonge 1994; Mattoo 2008).

Of the four amino acids that escape into the urine, only cystine causes trouble. Lysine, arginine and ornithine dissolve easily; cystine does not. A 2008 review states that "the only clinically significant manifestation is recurrent nephrolithiasis secondary to the poor solubility of cystine in urine" (Mattoo 2008). Cystine is two molecules of the amino acid cysteine joined by a sulfur-to-sulfur bond; the story of how it was first found in a bladder stone in 1810 is told on the Cysteine history page.

Cystinuria has a long place in medical history. In his 1908 Croonian Lectures, the physician Archibald Garrod used it as one of four examples of an "inborn error of metabolism", alongside albinism, alkaptonuria and pentosuria (Scriver 2008).

Two Genes and Three Types

The transporter is built from two protein parts, and each part is made by a different gene. SLC3A1, on chromosome 2, makes the heavy part (called rBAT); SLC7A9, on chromosome 19, makes the light part (Eggermann 2012). In 1994 a team reported six mutations in the rBAT gene in families with cystinuria; they accounted for 30% of the cystinuria chromosomes studied, and the commonest one nearly abolished the transporter's activity in frog egg cells (Calonge 1994).

An international consortium gathered genetic and clinical data on 224 people with cystinuria and proposed the classification used today (Dello Strologo 2002):

The same study looked at 189 carriers with one faulty gene. All SLC3A1 carriers and 14% of SLC7A9 carriers had normal urine amino acid levels; the remaining SLC7A9 carriers passed raised amounts (Dello Strologo 2002). This is why cystinuria is described as autosomal recessive for SLC3A1 but variable for SLC7A9, where clinical severity can differ even inside one family (Eggermann 2012). A 2020 US consensus statement describes the disorder as having "both autosomal recessive and incompletely dominant inheritance" (Eisner 2020).

Genetic testing finds the mutations in more than 85% of patients, a rate that varies with ethnic origin (Eggermann 2012). A rarer condition, the hypotonia-cystinuria syndrome, comes from a deletion on chromosome 2 that removes SLC3A1 together with a neighbouring gene, PREPL (Eggermann 2012).

How Common It Is

A 2025 review estimates the mean worldwide frequency of cystinuria at 1 in 7,000, with "significant ethnogeographic variation in prevalence" (Iuliano 2025). A US review calls it "the most common genetic cause of recurrent kidney stones" (Azer 2023).

Even so, cystine stones are a small share of all stones, because ordinary calcium stones are so common. Figures in the literature differ a little:

The common thread is that cystine stones are rare in adults but make up a noticeably larger share of the stones found in children.

How Cystine Stones Form

A stone forms when more cystine is dissolved in the urine than the urine can hold. Reviews give the solubility limit as about 250 mg of cystine per litre of urine, and describe the goal of treatment as bringing the urinary cystine concentration below that limit (Sakhaee 1994). The same figure, 250 mg/L, is the target written into US tiopronin labels (see the thiol drugs section below). Insoluble cystine falls out of solution as flat, six-sided (hexagonal) crystals that can grow together into larger stones (Mattoo 2008).

Two things move urine away from that limit: more water, which lowers the concentration, and a more alkaline urine, which raises how much cystine can stay dissolved. In the French series, crystals were studied in 89 patients. Compared with urine at pH 6.5 or lower, the odds of cystine crystals were about half at pH 7.0–7.5 (odds ratio 0.52) and about a quarter at pH 7.5–8.0 (odds ratio 0.26). More concentrated urine had the opposite effect: urine with a specific gravity of 1.011–1.014 carried 11 times the odds of cystine crystals seen at 1.005 or below (Prot-Bertoye 2019).

The alkaline side has its own limit. In the same study a urine pH above 8.0 raised the odds of calcium phosphate crystals about six-fold (odds ratio 6.09), which is why the authors set a target of pH above 7.5 "while warning about calcium-phosphate crystallization" (Prot-Bertoye 2019).

How much cystine a person passes does not line up neatly with how many stones they form. The international consortium found that "stone events do not correlate with amino acid urinary excretion" (Dello Strologo 2002).

When Stones Usually Begin

Older reviews state that cystine stones "frequently occur in the second or third decade of life, with an occasional occurrence in infancy and in old age" (Sakhaee 1994). The French national series gives the most detailed figures: the median age at first symptoms was 16.7 years, but the range ran from 0.3 to 72.1 years, and the median delay before diagnosis was 1.3 years, with some people waiting up to 45.7 years (Prot-Bertoye 2015).

In a US children's hospital cohort of 23 patients, the median age at presentation was 12 years. Pain was the commonest first symptom (13 of 23), followed by nausea or vomiting, visible blood in the urine and fever; one child arrived with acute kidney failure (Varda 2016). A case report from Spain describes the opposite end: an elderly man with no earlier stone history whose first episode of colic led to the diagnosis (Pierna 2020).

The disease is more severe in males than in females, according to the international consortium's clinical data (Dello Strologo 2002).

How It Is Diagnosed

Sources describe three main routes to the diagnosis:

Genetic testing of SLC3A1 and SLC7A9 confirms the type, and the European recommendation covers when it is used (Servais 2021; Eggermann 2012). Brothers and sisters of a known patient are often tested: in the US children's cohort five patients were found through sibling screening, and four of those five were managed with medical treatment alone (Varda 2016).

For follow-up, recent reviews describe a test called cystine capacity, which measures whether a person's urine can still dissolve added cystine (a positive number) or is already oversaturated and drops cystine out (a negative number). Reviewers treat it as a key recent advance in monitoring (Azer 2023; Zambudio Munuera 2026).

Fluid and Urine Alkalinisation

Both the 2020 US consensus statement and the 2021 European recommendation describe a step-by-step approach. It begins with fluid intake and diet changes; if stones keep forming, the next step is to make the urine more alkaline, and the step after that is a cystine-binding thiol drug (Eisner 2020; Servais 2021).

Fluid

A French centre followed 27 adults for a mean of 11.6 years on high fluid intake and alkali, with a thiol drug added when stones kept forming. Fifteen patients needed no further stone procedures. The patients whose stones stopped had a mean urine volume of 3,151 mL a day, against 2,446 mL a day in those whose stones continued, and the authors concluded that a daily urine volume above 3 litres is "essential for therapeutic success regardless of whether thiol derivatives are administered" (Barbey 2000). A 2024 systematic review of 14 studies reports that first-line therapy raised urine volume above 3 L a day and pH above 7.0 and was associated with less stone formation (Bhatt 2024).

Alkali

Because urinary sodium and cystine rise together, potassium citrate has become the preferred sodium-free alkali, according to a Swedish research group (Fjellstedt 2001). Their study in 14 patients compared it with sodium bicarbonate, two weeks on each. Both raised urine pH to a similar degree, but sodium bicarbonate raised urinary sodium. Plasma potassium was higher on potassium citrate and one patient developed mild hyperkalaemia (5.0 mmol/L); the authors limited their conclusion to people without severe kidney impairment (Fjellstedt 2001).

Stomach and bowel side effects were reported in 12.3% of French patients on potassium bicarbonate, 10.4% on potassium citrate and 2.6% on sodium bicarbonate (Prot-Bertoye 2019).

Salt and Protein in the Diet

A 2008 review lists "dietary restriction of salt and animal protein" among the standard prevention measures (Mattoo 2008), and both guideline documents include diet in their first step (Eisner 2020; Servais 2021). One reason given is that cystine transport across the kidney tubule is coupled to the transport of sodium (Lindell 1995).

The direct evidence is small and not fully consistent:

No trial was found that tested a particular diet pattern against stone recurrence in cystinuria. Lysine shares the faulty transporter; the theoretical question of lysine supplements in cystinuria is discussed on the lysine and arginine page.

Thiol Drugs: Tiopronin and D-Penicillamine

Thiol drugs carry a reactive sulfur group. They split cystine into two halves and bond to one of them, forming a "mixed disulfide" that leaves in the urine in place of free cystine (Harbar 1986; Moussa 2020). The two in long use are tiopronin (called alpha-mercaptopropionylglycine in older papers) and D-penicillamine.

How well they work

Side effects

What the US tiopronin labels state

The US Food and Drug Administration (FDA) labels for tiopronin, read for this page, state the following:

The Captopril Evidence

Captopril is a blood pressure drug (an angiotensin-converting enzyme inhibitor) that, like tiopronin, carries a sulfur group. It can form a captopril–cysteine compound that, according to a 1987 report, is 200 times more soluble than cystine (Sloand 1987). The evidence pulls in both directions:

All of these are case reports, letters or small uncontrolled series. No randomised trial of captopril in cystinuria was found for this page.

Surgery to Remove Stones

Most people with cystinuria have at least one stone operation. In the French national series, 81.8% had undergone at least one urological procedure (Prot-Bertoye 2015). A US study comparing 52 cystine stone formers with 3,215 people with ordinary stones found 4.0 procedures per unit of time at risk before treatment against 1.86 for ordinary stones; on treatment both rates fell, to 0.88 and 0.23 (Worcester 2006).

Cystine stones are hard for shock-wave lithotripsy, the method that breaks stones from outside the body (Worcester 2006). The methods described in the literature are therefore mainly:

The type of surgery matters for the long run. In a US comparison, a higher number of open stone operations and kidney removal were each linked to higher blood creatinine, a marker of lower kidney function, and 14.1% of cystinuric patients had lost a kidney against 2.9% of calcium oxalate stone formers. The authors concluded that a minimally invasive approach is preferred when stones need removing (Assimos 2002).

Kidney Function and Recurrence

Kidney function

Reviews disagree in tone about the long-term kidney outlook. A 2025 review describes the prognosis as favourable and says kidney failure is brought on "very rarely", mainly by poor adherence, repeated stones and repeated interventions (Iuliano 2025). The large clinical series show a less settled picture:

Recurrence

Newer Agents Under Study

Because the standard drugs are often poorly tolerated, several new approaches are being tested. None has reached a randomised trial with stone outcomes in people.

Alpha-lipoic acid — evidence: mice and two case reports

Alpha-lipoic acid is a nutritional supplement. In a mouse model lacking the SLC3A1 gene, it prevented cystine stones by making urinary cystine more soluble (Zee 2017). Two children aged 6 and 15, already taking potassium citrate, were given alpha-lipoic acid; both tolerated it, their urine's cystine capacity improved, and in one an existing stone disappeared after two months (Cil 2020). A 2026 study in a new mouse model carrying the commonest human SLC7A9 mutation found that alpha-lipoic acid reduced stone burden and inflammation in mice but also caused damage to the lining of the urinary tract (Bhatt 2026).

Tolvaptan — evidence: mice and an eight-day pilot

Tolvaptan blocks the hormone that makes the kidneys hold on to water, so it produces very large volumes of dilute urine. In mice with cystinuria it increased urine volume and slowed stone growth over 30 days (Bai 2021). In a pilot study of four people aged 13 to 24, eight days of tolvaptan turned cystine capacity from negative to positive in three of the four, and urine volume reached between 2.8 and 11.74 litres a day on the higher dose. Blood salts and liver tests stayed normal, but thirst was extreme, rated 9 out of 10 (Nelson 2020).

Crystal-growth inhibitors — evidence: laboratory and mice

These molecules are designed to stick to the surface of a growing cystine crystal and block further growth. In 2010, microscope studies showed that L-cystine dimethyl ester and L-cystine methyl ester sharply slowed cystine crystal growth in the laboratory (Rimer 2010). A later compound, reported in 2024, was about 120 times more potent than L-cystine dimethyl ester at blocking crystallisation, was absorbed when taken by mouth, and prevented stones in mice lacking SLC3A1 (Hu 2024).

Other ideas

A 2023 review lists cystine mimetics, gene therapy, vasopressin-receptor blockers such as tolvaptan, and sodium–glucose cotransporter 2 inhibitors as future research directions (Azer 2023). A 2026 review calls oral N-acetylcysteine a "rational candidate for formal prospective evaluation" but notes that robust trial evidence in cystinuria is lacking (Zambudio Munuera 2026); the older N-acetylcysteine findings are on the N-Acetylcysteine and Kidney Health page.

What Is Not Known

Key Research Papers

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PubMed Topic Searches

  1. PubMed: cystinuria
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  3. PubMed: cystinuria and chronic kidney disease
  4. PubMed: cystinuria genes SLC3A1 and SLC7A9
  5. PubMed: cystine stone surgery
  6. PubMed: cystinuria and alpha-lipoic acid

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