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A Functional Medicine Kidney Stone Protocol: Testing, Supplements, and Treatment Options

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A Functional Medicine Kidney Stone Protocol: Testing, Supplements, and Treatment Options

Kidney stones lead to a condition known as nephrolithiasis or urolithiasis. Stones or renal calculi occur in the kidneys when hard deposits made of crystals are formed from different types of minerals and salts that concentrate in the urine. Over time, these crystals can concentrate and grow into stones.

When kidney stones begin to move through the urinary tract, they cause pain in the side or back, blood in the urine, and nausea/vomiting. In most cases, these stones do not usually cause permanent damage if they're recognized in a timely manner, although the pain can be severe. Occasionally, kidney stones can lodge at points in the urinary tract and lead to complications such as urinary tract infections and kidney damage.

Kidney stones are a common condition and one of the most common urinary tract disorders. Around 12% of the world's population experience kidney stones at some point, and the rates are increasing. Men are more frequently impacted than women. Although kidney stones are common in otherwise "healthy" people, those with high blood pressure, diabetes, and obesity are at an increased risk. Once someone develops a stone, they are more likely to have more in the future.


What are Kidney Stones?

The kidneys normally remove waste from the blood and excrete these waste products from the body by dissolving them in the urine. When too high of a concentration of certain minerals and salts such as calcium, oxalate, urate, cystine, xanthine, and phosphate occur in the urine relative to too little liquid, crystals can begin to form. These crystals attract other elements and join together to form a solid mass that grows larger and forms a kidney stone unless it's passed through the urine, or the growth is halted by other substances.

Urolithiasis is a condition where stones form anywhere inside the urinary tract, from the kidneys to the urethra. When these stones are located inside the kidneys, nephrolithiasis or kidney stones develop. Kidney stones are hard irregularly-shaped pebble-like collections of crystals made up of minerals and salts that concentrate in the urine. They could be as small as a speck of sand or grow up to the size of a golf ball.

The four main kinds of kidney stones are calcium oxalate, uric acid, struvite, and cystine.

Calcium oxalate stones form when calcium and oxalate combine in the urine and are the most common type of kidney stones. These kinds of stones are more likely to form when the urine contains high amounts of calcium or oxalate or insufficient fluid. Too much calcium builds up in the urine when large quantities are absorbed from the diet or reabsorbed from the bones, or the kidneys have issues regulating how much calcium is excreted.

Oxalates are absorbed through the diet from eating large amounts of beets, potatoes, coffee, chocolate, spinach, rhubarb, cranberries, beans, peanuts, and other high-oxalate foods. The liver also makes oxalates in a process that increases with the consumption of ascorbic acid or high doses of vitamin C. Oxalate production is also increased with an imbalanced microbiome or other conditions that increase inflammation in the gut such as inflammatory bowel disease or prior intestinal surgery.

Calcium stones can also be composed of calcium phosphate. These types of stones are usually due to issues with the functioning of the urinary system.

Struvite kidney stones are composed of a mixture of magnesium, ammonium, phosphate, and calcium carbonate. Certain urinary tract infections involve bacteria that can produce ammonia, making the urine less acidic or more alkaline. Struvite stones can form when the urine becomes more alkaline, which favors crystal formation, and can grow quickly and become very large.

When too much purine concentrates in the urine, uric acid stones may form. High concentrations of purines are found in foods such as beef, poultry, pork, fish, organ meats like liver, and shellfish. When these foods are consumed frequently or in large quantities, this leads to a higher production of monosodium urate that can build up in the urine, causing stones due to high protein consumption, dehydration or fluid loss from diarrhea or malabsorption, genetic factors, or metabolic factors in those with diabetes or metabolic syndrome.

In those with a hereditary disorder called cystinuria, the kidneys will excrete too much of the amino acid cysteine. Cystine kidney stones form when cystine crystals concentrate and form stones in the urine. Since these stones are due to a genetic disorder, they tend to form repeatedly and are typically larger than other kidney stones.

Kidney Stones Symptoms

Very small stones may sometimes move out of the body without causing too much pain by traveling down the urinary tract with the urine through the ureter or tube, which connects the kidney to the urethra from which urine is expelled. Larger stones and those that don't move through completely can cause a blockage that leads to a back-up of urine in the kidney, bladder, ureter, or urethra that causes swelling, spasms, and pain.

Kidney stone pain is often severe and sharp, focused in the side and back below the ribs, and may radiate to the lower abdomen and groin. Due to spasms, this pain may come in waves and fluctuate in intensity. It can also move around as the stone passes through the urinary tract. There may also be burning or pain while urinating.

In addition to this pain, common symptoms of kidney stones include:

  • pink, brown, or red urine from blood in the urine
  • an increased urge to urinate or urinating more often than usual or in frequent small amounts
  • nausea and vomiting
  • fever and chills
  • urine that smells bad
  • cloudy urine

What Causes Kidney Stones?

Many factors contribute to kidney stone formation. Stones form when the urine becomes more concentrated due to insufficient water diluting crystal-forming substances, including calcium, oxalate, and uric acid. In addition, stones are more likely to form when the urine does not have high enough concentrations of substances that normally help to prevent crystals from sticking together.

Therefore, dehydration from not drinking enough water or due to diarrhea, vomiting, or malabsorption increase the risk of stone formation. Similarly, eating a diet rich in substances that form stones, like oxalates in spinach, purines in meat and shellfish, and phosphate in meat, fish, beans, and other protein-rich foods, makes stones more likely to form. Diets high in salt/sodium and processed sugars like fructose and corn syrup also increase the risk of stone formation.

On the other hand, dietary deficiencies of chelating agents like citrate, fiber, and alkaline foods that help reduce the concentration of stone-forming crystals also increase risk.

If you or any family member has experienced kidney stones previously, you are at a higher risk. In addition, certain medical conditions influence the levels of the crystals that make up kidney stones. For example, altered calcium metabolism occurs in metabolic disorders such as hypercalciuria (high calcium) and hyperparathyroidism. While those with gout and diabetes tend to have higher uric acid levels, predisposing them to uric acid stones.

With inflammatory bowel disease (IBD) or chronic diarrhea from other causes, kidney stones are more common due to chronic inflammation and malabsorption. These conditions involve several factors that increase kidney stone risk: poor absorption of citrate, magnesium, and fats that normally help to bind calcium to help excrete excess calcium oxalate in stools instead of requiring the kidneys to remove these oxalates in the urine; imbalances in the gastrointestinal microbiome with fewer oxalate-fermenting bacterium Oxalobacter fromigenes; and loss of water and salt due to chronic diarrhea that contributes to more concentrated urine.

Imbalances in the gut microbiome, like dysbiosis or small intestinal bacterial overgrowth (SIBO), can also give rise to elevated uric acid levels and the risk of kidney stones. Chronic stress can contribute to imbalances in gut bacteria and inflammation while increasing uric acid levels in the body and making kidney stones more likely.

Being overweight and gaining weight also increases the risk of kidney stones, especially in women. Obesity, high blood pressure, and hypothyroidism put stress on the kidneys, making it more challenging to eliminate uric acid, calcium, and other waste products from the body.

Several medications can raise the risk of developing kidney stones, including diuretics (water pills), excessive use of laxatives, large doses of citric acid/vitamin C supplements, calcium-based antacids, and antibiotics like ciprofloxacin and ceftriaxone.

How Are Kidney Stones Diagnosed?

Alongside a full medical history and physical examination, a kidney ultrasound scan can assess the size and location as well as possible obstruction of the urinary tract by a kidney stone. Abdominal X-rays, intravenous pyelogram (IVP), retrograde pyelogram, MRI scan of the abdomen and kidneys, or an abdominal CT scan can also be used to visualize the urinary tract.

Laboratory testing of the blood and urine helps to assess kidney function and the levels of crystal-forming substances in the blood and urine, as well as investigate potential underlying factors contributing to the development of stones.

Functional Medicine Labs to Test for Root Cause of Kidney Stones and Help Individualize Treatment

Functional medicine laboratory tests can measure the levels of crystal-forming substances in the blood and urine, evaluate the function of the kidneys, look at hydration status, and analyze the state of the gut and microbiome. These tests help provide an assessment of how the kidneys are functioning and metabolic factors that may underlie the development of kidney stones to help guide treatment.

Blood Testing for Calcium, Phosphorus, and Uric Acid

Laboratory testing can assess various biochemical issues. Elevated uric acid and calcium in the blood increase the risk of kidney stones. Similarly, alterations in phosphorus balance contribute to calcium kidney stones.

Uric acid, phosphorus, and calcium can be measured in the blood to assess their balance in the body. These levels can be evaluated along with parathyroid hormone, which increases the reabsorption ofcalcium while increasing the excretion of phosphorus, and vitamin D levels to assess biochemical imbalances involving calcium and phosphorus metabolism.

Vitamin Levels

Vitamin A deficiency, vitamin K2 deficiency, and vitamin D excess all influence calcium metabolism in ways that can increase the risk of kidney stone development. Levels of vitamin A, vitamin D, and vitamin K2 can be assessed via the blood.

Magnesium and B6 deficiencies are associated with an increased risk of kidney stones as these nutrients are needed for metabolizing and removing oxalates from the body. Serum magnesium and vitamin B6 testing can help establish levels in the body to guide supplementation if needed.

Kidney Function Testing

Blood testing can evaluate how well the kidneys are functioning. Blood urea nitrogen (BUN) measures the amount of urea nitrogen in the blood, which reflects how well the kidneys are functioning to remove wastes. Similarly, creatinine and glomerular filtration rate can also be measured via the blood to assess kidney functioning.


The urine can be tested to look for crystals, bacteria, blood, and white cells to evaluate levels of wastes and minerals and any signs of infection. A 24-hour urine collection test, including measuring calcium and urea, may be used to assess if too many stone-forming minerals or too few stone-preventing substances are being excreted in the urine.

Measure Hydration Status and Metabolic Balance

A complete metabolic profile provides a look at hydration status, blood sugar balance, and kidney function to assess these factors which can contribute to the risk of kidney stones.

Comprehensive Gut Test

Since imbalanced gut bacteria can decrease the breakdown and clearance of uric acid and oxalates from the body and lead to a higher risk of stones, a comprehensive gut test can provide insights that guide treatment. The Gut Zoomer stool test evaluates microbes in the digestive tract to assess overall balance, conditions like SIBO, metabolic imbalances, and functional digestive status.

Small Intestinal Bacterial Overgrowth (SIBO)

Since SIBO can contribute to problems breaking down uric acid, a breath test can evaluate the overgrowth of bacteria that do not normally belong in the small intestine. The 3-hour SIBO assessment is a non-invasive breath test that measures hydrogen and methane to evaluate bacterial overgrowth in the small intestine.

Thyroid Function

A complete Thyroid Panel, which includes thyroid-stimulating hormone (TSH), T3 (free and total), T4 (free and total), and reverse T3, should be assessed using functional medicine ranges since thyroid hormone imbalances contribute to uric acid buildup in the blood.

Stone Analysis

Laboratory analysis of passed stones can help assess the specific type and makeup of kidney stones and guide treatment to prevent future stones.


Conventional Medicine Kidney Stones Treatment

Treatment of kidney stones is tailored to their size, type, and location, as well as addressing any complications that develop. Often, uncomplicated kidney stones can pass on their own and only require conservative treatment with adequate hydration and pain control.  

When stones are too large or do not move through the urinary tract on their own, they can be targeted with interventions to remove them or help them pass.

Shockwave lithotripsy uses high-energy sound waves to break up the stones so that the smaller pieces can pass through the urinary system and out of the body.  

Alternatively, a physician may use a type of camera scope known as a cystoscope to look inside your urethra and bladder to find a stone or a longer ureteroscope to visualize the lining of the ureters and kidneys and search for stones or damage. Once a stone is found, the scope can allow for its removal or break up into smaller pieces to remove or pass.

Similarly, when larger stones lodge in the kidneys, doctors can use a nephroscope inserted directly into the kidney via a small cut made in the back to locate and remove a kidney stone (percutaneous nephrolithotomy).

Functional Medicine Treatment Protocol for Kidney Stones

A functional medicine approach helps to treat recurrent kidney stones and prevents the future development of stones by uncovering and addressing underlying contributing factors. This treatment protocol should be individualized and tailored to the type of stone and other patient characteristics. Passed stones can be collected by straining the urine and evaluated for composition.

Therapeutic Diet and Nutrition Considerations for Kidney Stones

A functional medicine approach incorporates dietary interventions that can help treat and prevent the formation of kidney stones.

Moderate Animal Protein

Eating animal proteins raises the amount of acids that the kidneys have to process, resulting in reduced excretion of substances that help to reduce the formation of kidney stones like citrate. Therefore, limiting animal protein in the diet can help prevent recurrent calcium stones.

Foods like shellfish, organ meats, commercially produced red meat and poultry, beer, and yeast are high in purines which are metabolized to produce uric acid, so reducing the intake of these foods can help to decrease the risk of uric acid stones.

Eat Fewer Oxalates

In people prone to forming calcium oxalate stones, reducing foods that are rich in oxalates, such as rhubarb, beets, okra, spinach, Swiss chard, sweet potatoes, nuts, tea, chocolate, black pepper, and soy products, may be helpful.

One way to reduce the risk of forming oxalate stones is to consume oxalate-rich foods together in a meal with foods rich in calcium. This makes it more likely that the oxalate and calcium from the foods will bind to one another in the digestive tract and be excreted in the stool instead of entering the kidneys, where they could form kidney stones. Cooking oxalate-rich foods can also help to reduce the oxalate content.

Stay Hydrated

Adequate and consistent hydration is essential for keeping the urine dilute of waste and regularly passing through the system. Hydration needs vary based on many individual factors. But it's generally recommended that people with a history of kidney stones drink enough water to pass about 2.1 quarts (2 liters) of light and clear urine a day.

Adding lemon to your water can have additional benefits. The citric acid found in lemons, limes, and other citrus fruits (not to be mistaken for ascorbic acid or vitamin C) inhibits stone formation.

Be Careful with Salt Intake

Since sodium and calcium share the same transport in the kidney, consuming high-sodium foods, like processed foods, increases the amount of calcium excreted in the urine. Therefore, a high-sodium diet can increase your chances of developing another stone. Restricting dietary salt intake reduces calcium excretion in the urine and helps to prevent recurrences of idiopathic calcium stones.

Avoid High Doses of Vitamin C Supplements

Taking high-dose vitamin C supplements can increase the number of oxalates produced in the body and therefore increase the risk for kidney stones. It is generally recommended to avoid excess amounts over 1000 mg/day.

Supplements Protocol for Kidney Stones

Along with diet, supplements can help treat and prevent kidney stones. A successful supplement protocol for kidney stones should be individualized for the specific patient, type of stone, and other contributing factors.


Magnesium is an essential mineral used for more than 300 biochemical reactions to occur in the human body. Magnesium helps to reduce the formation of kidney stones by inhibiting the absorption of dietary oxalate from the gut lumen and inhibiting the formation of calcium oxalate crystals in the urine. While research shows some mixed results, ensuring adequate magnesium intake via supplementation or Epsom salts (magnesium sulfate) baths may help prevent stones, especially in those who are deficient in magnesium. Studies suggest that adding magnesium to potassium citrate therapy improves the prevention of kidney stone formation.

Dose: 200 to 500 mg a day of magnesium oxide, hydroxide, or citrate

Duration: 12 weeks-3 years

Potassium Citrate

Since calcium oxalate, uric acid, and cystine stones tend to form in acidic urine, potassium citrate protects against these types of stones. It does so by alkalinizing urine (metabolizing it to bicarbonate), binding calcium in the gut and urine, and inhibiting calcium oxalate crystallization.

Potassium citrate can be used to alkalinize the urine, increase urine citrate, inhibit the accumulation of calcium oxalate and calcium phosphate crystals, and lower the risk of kidney stones alone or in combination with magnesium which has proven to yield superior results.

Dose: 15 to 30 milliequivalents (mEq) two times per day or 10 to 20 mEq three times a day (1200–2400 mg per day)

Duration: varies depending on blood monitoring of potassium levels of urine pH


The gut microbiome is vital for oxalate breakdown and metabolism, preventing kidney stones. A study showed that the average urine oxalate levels fell by 19% after one month of taking 8.5 billion bacteria daily and by 24% at a dosage of two each day during the second month of therapy.

Dose: 8.5 billion bacteria of Lactobacillus and/or Bifidobacterium strains once or twice daily

Duration: 4+ weeks

Vitamin B6/Pyridoxine

Vitamin B6 (pyridoxine) is required for over 100 different reactions in the body. A deficiency in this vitamin may increase urine oxalate and kidney stone risk. Supplementation with oral B6 can significantly lower urinary oxalate levels in people who form oxalate kidney stones. A large 14-year study of over 85,000 women found that kidney stone risk was 34% lower in women consuming the most vitamin B6 daily from diet and supplements than those who consumed the least. Pyridoxine supplementation may be combined with magnesium supplementation in some cases, with studies showing that daily oral supplements of 200 mg of magnesium oxide and 10 mg of pyridoxine for five years or more resulted in no recurrence or decreased recurrence of stone formation in patients with recurrent calcium oxalate kidney stones.

Dose: 10 mg oral tablets/day

Duration: 60+ days up to 5 years

Alpha Lipoic Acid (ALA)

Alpha lipoic acid (ALA) is a fat and water-soluble antioxidant that helps prevent tissues from free radical damage and supports the body's ability to "recycle" other antioxidants for further use. In addition to helping to prevent kidney stones and kidney damage, ALA may also reduce intestinal inflammation in inflammatory bowel disease. This factor can increase the risk of kidney stone formation. In experimental models, ALA has been shown to improve the excretion of cysteine to prevent the formation of kidney stones, with clinical trials in humans ongoing.

Dose: 300 mg orally twice per day OR 1200 mg alpha lipoic acid orally daily

Duration: three years

How to Prevent Kidney Stones?

Approaches to prevent the future development of kidney stones are tailored to the type of stone and underlying medical issues and contributing factors. Passed stones can be collected by straining the urine and evaluated for composition.

Based on the type of stone, dietary adjustments can be implemented in order to lower the risk of future stone development. For all kinds of stones, drinking enough water to dilute your urine can help flush away minerals that might form stones.

Depending on your type of kidney stone and the laboratory testing results, a personalized dietary and supplement protocol can be implemented to prevent any future stones from developing.

For example, some people who form calcium oxalate kidney stones can prevent future stones by following a low-oxalate diet, avoiding high-dose vitamin C supplements, and supplementing with potassium citrate to alkalinize the urine and inhibit the formation and growth of calcium crystals.

When to Retest Labs

It is essential to regularly monitor laboratory levels of supplemented nutrients and other relevant parameters to monitor treatment progress and ensure its ongoing effectiveness. While the frequency of retesting may vary based on individual needs, underlying factors, and the treatment regimen implemented, retesting is generally performed every 3 to 6 months or as needed, based on the patient's response to the treatment and any changes in symptoms.



Kidney stones are composed of accumulated mineral salts that form crystal clumps. The most common kidney stone type is calcium oxalate or phosphate. Other stones may be formed from uric acid, struvite, and cystine.

Kidney stones can cause significant pain when they grow large enough or move through the urinary tract. In addition, they may cause blood in the urine, increased urinary frequency, and nausea/vomiting.

Common risk factors for developing kidney stones include dehydration, high intake of animal-derived protein, high oxalate intake from foods such as beans, beer, berries, coffee, chocolate, some nuts, some teas, spinach, beets, and potatoes), and high salt intake. While these stones are common in otherwise healthy individuals, a family history of kidney stones and various medical conditions like inflammatory bowel disease, obesity, and hypertension increase the risk of stones developing.

While symptomatic kidney stones generally require acute medical attention, functional medicine can utilize testing and treatment approaches to address underlying contributors and prevent a recurrence. Laboratory testing can measure levels of various substances that make up kidney stones and assess kidney function. Urine testing can look for crystals, bacteria, blood, and white cells to evaluate levels of wastes and minerals and signs of infection.

An anti-inflammatory diet that incorporates calcium-rich foods and lemon water for adequate hydration while avoiding excessive animal protein, sodium, processed sugars, and high-oxalate foods like spinach, rhubarb, chocolate, and black tea can help prevent kidney stones from forming. In addition, maintaining a healthy gut microbiome and getting enough magnesium may reduce the risk of stones.

Along with diet, supplements can help treat and prevent kidney stones. A successful supplement protocol for kidney stones should be individualized for the specific patient, type of stone, and other contributing factors. It may incorporate magnesium, potassium citrate, probiotics, pyridoxine, or alpha lipoic acid.

The information provided is not intended to be a substitute for professional medical advice. Always consult with your doctor or other qualified healthcare provider before taking any dietary supplement or making any changes to your diet or exercise routine.
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