Crystals in Urine: Causes, Home Treatments, and When To See a Doctor

Crystals in Urine: Causes and Effective Natural Treatments

Crystals in urine are usually detected in a urine analysis. The only visible sign you may notice if you have urinary crystals is cloudy urine; however, some types of crystals in urine are not visible at all without a microscope. Your kidneys are needed to filter out waste products from the body and excess fluid, and these end up in urine. The kidneys are also responsible for regulating salt, urinary acid content, and other minerals in the urine. If you have kidney problems or your urine is too concentrated, urinalysis may show up that there are too many crystal substances in your pee.

Some simple reasons for the presence of urinary crystals are because of dehydration or the side effect of medicines. In these cases, drinking more water can help return your urine to its normal color and mineral content. Doctors will usually check for the presence of an abnormally high number of crystal-like substances in urine if they suspect you have a urinary tract infection, kidney stones, or some other kidney dysfunction. In more serious cases, it’s important to treat the underlying cause of urine that contains crystal-like substances.

This article looks at the various reasons why crystals can appear in a urine test and what you can do to treat the problem. First, let’s look at what urinary crystals are and why having them in your urine can sometimes be a cause for concern.

What are Urinary Crystals?

The medical name for crystals in urine is crystalluria. Healthy urine may contain a few microscopic crystals and they may also form after you have given a urine sample. According to the American Association for Clinical Chemistry, the number and type of crystals that form in urine are connected with urine pH levels, the concentration of substances in urine, and urine temperature.1

Common Types of Crystals in Urine

When performing a urinalysis, doctors will look at the shape and structure of the urinary crystals to determine their type. Here are some of the common types of crystals that show up in urine and what they mean.

Uric acid crystals. Dr. Anne Poinier on WebMD says that uric acid is usually excreted when you pee. High levels of uric acid crystals can form kidney stones and cause inflammation in joints.2

Calcium oxalate crystals. These types of crystals can form if the blood contains high levels of calcium, oxalate (salts that occur in many plants and nuts), cystine (a type of amino acid), and too little fluid. According to the journal Calcified Tissue International, this type of urinary crystal can form into kidney stones.3

Cystine crystals. If the amino acid cystine leaks into your urine, it can show up as cystine crystals in a urinalysis. According to MedicineNet, this is a common inherited condition that can cause frequent bladder and kidney stones. Urologist, Dr. Michael Wolff says that one of the best ways to prevent the buildup of crystal substances is to drink plenty of fluids.4

Phosphate crystals. Your kidneys are responsible for the amount of phosphorus in your body. Dr. Gregory Thompson on WebMD says that high levels of phosphate crystals in urine can be caused by eating high levels of protein-rich food, having too much vitamin D, or an overactive parathyroid gland. This often results in cloudy urine.5

Sulfur crystals. Sulfur crystals form as a result of taking antibiotics. According to Dr. Jay Marks on MedicineNet, high levels of sulfur crystals in the urine can damage the kidneys. That is why it’s important to keep well hydrated if you are taking a course of antibiotics.6

Cholesterol crystals. If your diet contains saturated fats, then cholesterol crystals can show up in your urine.7

Triple phosphate crystals. Composed of ammonium magnesium phosphate, these types of urinary crystals are often seen in cases of urinary tract infections and can also be associated with increased levels of urinary leukocytes.

Symptoms of Crystals in Urine

A urinalysis that shows high levels of crystals is usually accompanied by different symptoms depending on the underlying cause. For example, if you have cloudy urine from not drinking enough fluids, you may have other signs of dehydration as well bubbles in your urine.

If a urinary tract infection or kidney stones are causing abnormally high levels of crystals to leak into the urine, you may also have a burning sensation when peeing, flank pain, and feel an unusually strong odor from your pee. Your urine test may also show up elevated nitrate levels in your urine.

Doctors from the Mayo Clinic say that too many uric acid crystals could also lead to gout. This will cause inflammation in your joints as the crystals collect there, especially in the big toe. You will notice redness and probably experience a lot of pain. For natural ways to relieve gout pain, please read how consuming tart cherry juice can give you relief from gout.

Causes of Crystals in Urine and What to Do About It

Let’s examine some of the causes of having crystallized urine and what you can do about it. At the end of the article, you can find some helpful advice on how to keep your urinary tract healthy and to avoid conditions that make crystal deposits form in the urine.


In order to flush waste products from your body and reduce the number of crystals in your urine, you need to drink enough fluids. Dehydration can have serious health consequences and can cause fatigue, spikes in blood pressure, and even kidney stones.

A study on the effects of dehydration on marathon runners found a higher concentration of urinary salts in urinalysis. Urine tests of marathon runners 11 days after racing showed elevated levels of oxalate dihydrate crystals in urine.7

The best way to make sure and prevent a buildup of urinary crystals is to drink enough fluids. Keeping well hydrated helps to flush toxins and mineral deposits from your kidneys. One way to boost your water intake is to try one of my infused water recipes. These refreshing drinks contain very little calories but are packed with goodness, vitamins, and minerals.

Urinary tract infection (UTI)

A urinary tract infection (UTI) can cause crystalluria, pain when urinating, a foul smell from urine, foamy urine, cloudy urine with sedimentdark colored pee and the urge to frequently use the bathroom. UTIs are caused when bacteria enter the urinary tract or you get an infection of the urethra.

According to the International Journal of Research in Medical Sciences, bacteria in the urinary tract can cause large numbers of calcium oxalate and amorphous urates in the urine sample.8 Doctors from the Mayo Clinic say that kidney stones or bladder stones, wiping from back to front, and a weakened immune system are some factors that can lead to a UTI.9  

To help treat a UTI at its early stages, doctors from the Mayo Clinic recommend drinking plenty of water to help flush out bacteria and dilute the concentration of urinary crystals.10 Other ways to treat a UTI naturally include taking D-mannose powder, increasing your intake of cranberries and blueberries, and drinking a glass or two of diluted apple cider vinegar every day.

These home remedies for urinary tract infections can only help treat the early stages of a UTI. If the infection progresses and you have a fever, dark-looking urine with a foul smell, and abdominal or pelvic discomfort, you should see your doctor.

Kidney or bladder stones

If uric acid crystals, calcium oxalate crystals, or cystine crystals don’t get flushed out of your urine, you could end up with kidney or bladder stones. If you have severe flank pain and find it painful to pee, your doctor will check for the presence of crystals in your urine.

The journal Kidney International published a report on the link between urinary crystals and kidney stones. The research found that people with crystalluria were more at risk from recurring kidney stones.11

One way to help get rid of kidney stones and dissolve the buildup of stone-forming crystals is to drink apple cider vinegar (ACV). One study into the effects of acetic acid (the main component of apple cider vinegar) on kidney stones found that they help to dissolve the mineral deposits.

To use apple cider vinegar to treat kidney stones, you should mix 2 teaspoons ACV in a 6-8 oz. glass of water. Drink frequently throughout the day. Continue drinking the ACV remedy until your symptoms of kidney stones or bladder stones have gone for good.

Another way to help stop crystallization of your urine is to drink baking soda water. Baking soda will make your urine more alkaline and prevent kidney stones forming. It is also a natural way to reduce the pain that debilitating gout causes.

Drinking baking soda will help increase your urinary pH levels, which is also associated with crystalluria. All you have to do is mix 1/2 teaspoon baking soda in a glass of water. Drink a few glasses in a 24-hour period.

Side effect of Medications

One of the causes of crystals in urine is taking certain medicines. As well as your liver, your kidneys play a role in metabolizing medications in the body. Depending on the interaction between various medications and the amount of fluid you drink, high levels of crystals in your urine could appear in urinalysis.

For example, the European Renal Association stated that medicines like antibiotics, antivirals, diuretics, and anti-epileptic drugs are known to cause crystallization of the urine. The side effect of these drugs causing a large number of crystals in urine can cause serious complications like urinary blockages, cloudy smelly urine, and renal dysfunction.12

If you are taking medication and you notice any changes to the color of your urine or you have symptoms like a burning sensation when you urinate, then you should discuss the matter with your doctor.

Change in urine pH levels

If your urine is too acidic or too alkaline, you are at risk of urinary crystallization. This could increase the risk of developing kidney stones, a urinary tract infection, or blockage in the urinary tract.

The Journal of Nephrology reported that urine that is too acidic usually results in an increase of uric acid and cystine crystals. However, urine that is more alkaline with high pH levels, tends to cause the crystallization of calcium and phosphate containing stones.13 Alkaline urine also causes triple phosphate crystals to develop and is associated with urinary tract infections.14

Drinking apple cider vinegar, although acidic in nature, actually helps to balance pH levels in the body as it helps the blood and urine become more alkaline once it is metabolized in the body.

Buildup of uric acid

A buildup of uric acid in the body can cause crystals to deposit in joints and cause gout or form into stones in the kidneys. According to Dr. William C. Shiel on eMedicineHealth, kidney dysfunction can hinder uric acid excretion in the urine.15 Also, research has found that eating a diet rich in protein and seafood increased uric acid whereas consuming plain yogurt every day helped to lower blood uric acid.16

How to Treat and Prevent Crystals in Urine

Apart from specific ways to treat medical conditions that can cause high levels of urine crystals, you can care for your urinary health daily.

The National Kidney Foundation recommends drinking plenty of water to help flush your kidneys and help them remove waste deposits from your body. If you exercise a lot or live in hot climates, then you may need to increase your fluid intake.17

Also, eating a healthy, balanced diet can prevent a buildup of certain salts and minerals that can crystallize in your urine. This includes not consuming excessive amounts of protein and reducing salt and sugar intake. Reducing the consumption of oxalate-rich foods like beets, greens, and sweet potatoes may be beneficial for people who form calcium oxalate stones, the leading type of kidney stones.18

Crystals in Urine – When to See a Doctor

You should call a doctor if symptoms of a urinary tract infection haven’t gone away within a day or two or you have extreme pain from a suspected kidney stone. Doctors at WebMD advise that some of the warning signs of these conditions are the following:20, 21

  • Pain just below your ribcage, your lower back, or lower abdomen
  • Nausea and vomiting
  • Fever
  • You notice blood in your urine
  • Burning when you urinate
  • Your urine is a cloudy or dark color

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Article Sources

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  3. Calcif Tissue Int. 1996 Jul;59(1):33-7.
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  5. WebMD. Phosphate in urine.
  6. MedicineNet. Sulfonamides.
  7. NLM. Understanding urine tests.
  8. Urolo Res. 1988 Mar;16(2):89-93.
  9. Int J Res Med Sci. 2015 May;3(5):1085-1090.
  10. MayoClinic. Urinary tract infection.
  11. MayoClinic. Urinary tract infection – lifestyle and home remedies.
  12. Kidney Int. 2005 May;67(5):1934-1943.
  13. Nephrol Dial Transplant. 1996 Feb;11(2):379-87.
  14. J Nephrol. 2010 Nov-Dec;23 Suppl 16:S165-9.
  15. AAFP. Urinalysis: A comprehensive review.
  16. eMedicineHealth. Gout.
  17. eMedicineHealth. What is gout?
  18. Kidney. 6 easy ways to prevent kidney stones.
  19. Kidney. Calcium oxalate stones.
  20. WebMD. Urinary tract infections.
  21. WebMD. Kidney stones.

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