Cystine Stones (Cystinuria): What They Are, Symptoms, Causes, Diagnosis, Treatment and Outlook — What You Need to Know
Updated: 25 minutes ago
Medically reviewed by Dr. Baraa Alnahhal, MD · Last reviewed: September 2026
Quick answer
Cystine stones are a rare type of kidney stone made of the amino acid cystine, caused by an inherited genetic condition called cystinuria. They tend to be larger than other kidney stones, often form repeatedly throughout life, and most frequently cause their first stones before age 20. Treatment focuses on prevention: high water intake, a low-sodium and lower animal-protein diet, and medications like tiopronin or d-penicillamine, with surgery reserved for large stones that cannot pass.
TL;DR
Cystinuria affects about 1 in 10,000 people and causes cystine to build up in urine, forming stones that account for only 1–2% of all kidney stones. The condition is lifelong and has no cure, but it is usually not life-threatening and rarely leads to kidney failure. Most people respond well to a treatment plan of hydration, diet changes, and medication, monitored with periodic urine testing.
What this guide can and cannot tell you: the numbers in this article come from a single, medically reviewed clinical source and are presented with attribution. No other statistics are used, and none are invented to fill gaps.
What are cystine stones?
Cystine stones are a type of kidney stone. A kidney stone is a hard mass made up of a collection of chemicals in your pee. Cystine stones are made of cystine, an amino acid in your body. When cystine does not reabsorb into your kidneys, it builds up and causes a cystine stone.
Amino acids are a type of protein building block that help repair your body's tissues, build muscle, and fight infection. People with cystinuria have a problem with how their kidneys absorb or process this particular amino acid.
These stones tend to be large and sometimes need to be removed surgically to prevent damage to your kidneys or urinary tract. Most people with cystine stones will develop several of them in their lifetimes. Fortunately, there are treatment options that do not involve surgery, including changing your diet or taking medication to balance the pH of your pee.
How common are cystine stones?
Cystine stones are rare. They account for 1% to 2% of all kidney stones, but they make up 6% to 8% of kidney stones in children. The underlying condition, cystinuria, affects about 1 in 10,000 people. More than 80% of people who get cystine stones get their first stones before age 20, although you can develop a cystine stone at any age.
Quick fact | Detail |
Condition type | Rare inherited kidney stone disorder |
Underlying condition | Cystinuria (autosomal recessive) |
Share of all kidney stones | 1% to 2% |
Share of kidney stones in children | 6% to 8% |
People affected | About 1 in 10,000 |
Age of first stones | More than 80% before age 20 |
Cure | None. Lifelong, but manageable |
Stone characteristics | Tend to be large; often recur throughout life |
What are the symptoms of cystine stones?
The symptoms of cystine stones are similar to those of other types of kidney stones, and you only feel symptoms if you have a stone. Symptoms can include a sharp pain in your side or back (typically on one side of your body), pain in your groin or abdomen, blood in your pee, vomiting and upset stomach, and pain when you pee (if the stone is near your bladder).
Because cystine stones tend to be larger than other types of kidney stones, a stuck stone may also cause a urinary tract infection (UTI).
What causes cystine stones?
People with a rare condition called cystinuria get cystine stones. Changes in the SLC3A1 and SLC7A9 genes cause you to be born with cystinuria. It makes it harder for your body to process cystine, which leads to it building up and forming stones. Cystine stones can get stuck anywhere in your urinary tract, such as your bladder or kidneys.
Cystinuria is an autosomal recessive gene condition that runs in your biological family. This means both parents need to have the gene for cystinuria to pass it to their biological child.
What is cystinuria?
Cystinuria is a rare, inherited condition (it runs in families) that causes cystine to build up in your pee. If you have cystinuria, your body has trouble dissolving cystine, which causes it to accumulate and form a cystine stone. It is a lifelong condition with no cure. You can only manage it with the right treatments, and it can cause you to develop multiple cystine stones throughout your life.
What are the complications of cystine stones?
Cystinuria is a condition you will have for life. Your healthcare provider can help you manage it with medications, dietary and lifestyle changes, and surgery, but you will be prone to getting cystine stones for the rest of your life. They can become quite painful, especially if you are waiting for one to pass.
Complication | What happens |
Kidney infections | A stuck stone can lead to infection in the kidney |
Blocked ureter | The tube that carries pee from your kidneys to your bladder becomes obstructed |
Urinary tract infections (UTIs) | Larger cystine stones are prone to becoming stuck and causing infections |
Kidney damage | Recurring stones and obstructions can harm the kidney |
How are cystine stones diagnosed?
Your healthcare provider diagnoses cystine stones by listening to your symptoms and getting your full medical history, including your family history. If you can collect a stone that has passed out of your body with your pee, your provider can send it to a lab for analysis, which identifies what chemical makes up the stone.
Diagnostic method | What it reveals |
Imaging tests (ultrasounds, CT scans) | Locate stones in the kidneys and urinary tract |
Urine tests (urinalysis) | Detect blood, signs of infection, and cystine levels |
Lab analysis of a passed stone | Identifies the exact chemical that makes up the stone |
How is cystine stone treatment managed?
A major part of treating cystine stones is preventing stones from forming in the first place. This involves reducing the amount of cystine in your pee. Your healthcare provider will likely recommend a mix of medication and changes to your eating habits to reduce the number of stones you get.
What medications treat cystine stones?
If your provider thinks a stone will pass on its own by drinking lots of water, they may recommend over-the-counter (OTC) pain medication like acetaminophen for discomfort. They may also recommend medications like tiopronin and d-penicillamine, which can help prevent the development of future stones.
What eating changes help prevent cystine stones?
Research shows people with cystinuria benefit from drinking more water, eating fruits and vegetables, and eating less salty food.
Dietary change | Why it helps |
Drink lots of water | Helps pass a cystine stone; providers may recommend up to 96 ounces a day, a glass every hour, or waking to drink at night |
Limit sodium (salt) | Reduces cystine buildup; may mean eliminating frozen or canned foods |
Cut back on animal protein (meat) | Swapping meat for plant-based protein helps reduce stone formation |
When is surgery needed for cystine stones?
Large stones can cause damage if they cannot pass through your urinary tract. These stones can be very painful and prevent the flow of pee out of your body.
Surgical option | How it works |
Ureteroscopy | A small, flexible camera is inserted up the urethra, bladder, and ureter to locate and remove the stone |
Percutaneous nephrolithotomy | A small incision is made in the skin of your back, and a tube is inserted into your kidney to remove the stone |
How do I know treatment is working?
Your healthcare provider may order a urinalysis to periodically check your cystine levels. This test can tell them if your treatment plan is working. It is possible to pass a cystine stone, but it requires careful monitoring and ongoing treatment.
What is the outlook for cystine stones?
Cystinuria is usually not life-threatening, and most people do not end up with kidney failure. It is important to work with your healthcare provider on a treatment that works for you. Most people respond well to treatment and can find a method that does not lead to kidney, bladder, or urinary tract damage.
Cystine stones can happen multiple times in your life. If you have cystinuria, you may need food-related changes and medication to prevent them. Your provider will monitor you and make sure you receive proper treatment for any new cystine stones to prevent damage to your urinary tract, kidneys, and bladder.
Can cystine stones be prevented?
Cystinuria is an inherited condition that you cannot prevent. But you can prevent the formation of cystine stones by following your healthcare provider's treatment plan.
Living with cystinuria
Because the condition is genetic, it is helpful for people who have cystinuria to receive genetic counseling if they wish to expand their families. The good news is that the condition is usually manageable with treatment and typically does not lead to kidney failure or serious damage to your urinary tract.
A note from the clinical source: Cystinuria is a lifelong condition that causes you to get cystine stones. Work with your healthcare provider on a treatment plan that prevents stones from developing.
When should I see my healthcare provider?
Talk to your healthcare provider if you experience any signs of a kidney stone. Some of the most common symptoms include pain in your abdomen, side, back, or groin area, nausea and vomiting, and painful urination.
Conclusion: a lifelong condition that is highly manageable
Cystine stones are a rare but repeatable type of kidney stone, caused by the inherited condition cystinuria. Most people with the condition develop their first stones before age 20 and may form stones multiple times throughout life. The outlook, however, is reassuring: the condition is usually not life-threatening, rarely causes kidney failure, and responds well to a disciplined prevention plan. The essentials are drinking large amounts of water, eating less salt and less animal protein, taking prescribed medication to block future stones, and keeping every urine-test follow-up, with surgery reserved for stones too large to pass.
Your next step: if you have been diagnosed with cystinuria or have symptoms of a kidney stone, work closely with your healthcare provider to build and follow a prevention plan. Since the condition is genetic, consider genetic counseling if you are planning to expand your family.
Frequently asked questions
What are cystine stones?
Cystine stones are a type of kidney stone made of the amino acid cystine. They form when cystine builds up in the urine instead of reabsorbing into the kidneys.
What causes cystine stones?
They are caused by cystinuria, a rare inherited condition. Changes in the SLC3A1 and SLC7A9 genes make the body unable to process cystine properly, so it builds up and forms stones.
What is cystinuria, and is it genetic?
Cystinuria is a rare, inherited, lifelong condition that affects about 1 in 10,000 people. It is autosomal recessive, meaning both biological parents need to carry the gene to pass it to their child. It has no cure but is manageable with treatment.
How common are cystine stones, and at what age do they start?
Cystine stones account for 1% to 2% of all kidney stones but 6% to 8% of kidney stones in children. More than 80% of people who get them have their first stones before age 20, though stones can develop at any age.
What do cystine stones look like?
Cystine stones tend to be larger than other types of kidney stones. Lab analysis of a passed stone is the definitive way to identify cystine as the stone's chemical makeup.
What are the symptoms of cystine stones?
Symptoms occur only when a stone is present and include sharp pain in the side or back (usually one side), groin or abdominal pain, blood in the pee, vomiting and upset stomach, and painful urination if the stone is near the bladder.
Do cystine stones cause infections?
Yes. Because they tend to be larger than other kidney stones, stuck cystine stones can cause urinary tract infections and kidney infections.
What are the complications of cystine stones?
Complications include kidney infections, a blocked ureter, urinary tract infections, and damage to the kidney.
Can cystine stones be cured?
No. Cystinuria is a lifelong condition with no cure. Stones can be treated and prevented, but the underlying condition is managed, not cured.
Is cystinuria life-threatening?
It is usually not life-threatening, and most people do not end up with kidney failure. Most people respond well to treatment that avoids damage to the kidneys, bladder, or urinary tract.
How are cystine stones diagnosed?
Through symptoms, medical and family history, imaging tests (ultrasounds and CT scans), urine tests, and lab analysis of a passed stone to identify its chemical makeup.
Can you pass a cystine stone on your own?
It is possible to pass a cystine stone by drinking lots of water, but it requires careful monitoring and ongoing treatment.
What medications are used for cystine stones?
Over-the-counter pain medication like acetaminophen can help with discomfort while a stone passes, and medications like tiopronin and d-penicillamine help prevent future stones.
How much water should I drink for cystine stones?
Your provider may recommend drinking 96 ounces of water in a day, a glass of water every hour, and/or waking up to drink water at night to help pass and prevent stones.
What foods should I avoid with cystinuria?
Providers recommend limiting sodium (salt), which may mean eliminating frozen or canned foods, and cutting back on animal protein (meat) in favor of plant-based protein. Research shows people with cystinuria benefit from eating fruits and vegetables, more water, and less salty food.
When is surgery needed for cystine stones?
Surgery is an option if medication and a modified eating plan are not enough to prevent stones or if the stones become large. Large stones can block urine flow and cause damage. The two main procedures are ureteroscopy and percutaneous nephrolithotomy.
How do I know my cystine stone treatment is working?
Your provider may order a urinalysis to periodically check your cystine levels, which tells them if the treatment plan is working.
Can you prevent cystine stones?
You cannot prevent cystinuria itself because it is inherited, but you can prevent stone formation by following your provider's treatment plan of hydration, diet changes, and medication.
Should I get genetic counseling for cystinuria?
Since the condition is genetic, it is helpful for people with cystinuria to receive genetic counseling if they wish to expand their families.
When should I see my provider about cystine stones?
Talk to your healthcare provider if you experience pain in your abdomen, side, back, or groin, nausea and vomiting, or painful urination, the common signs of a kidney stone.
External references
Cleveland Clinic: Cystine Stones (primary source, medically reviewed, last updated Jul 25, 2024)
References
Disclaimer: This article is for general educational purposes only and does not constitute medical advice. It is based on a single referenced clinical source and should not replace professional diagnosis or treatment. If you have symptoms of a kidney stone or have been diagnosed with cystinuria, please consult a qualified healthcare provider.
Comments