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Crystals in urine

Crystals in urine
portrait of Fernando Martínez Sáez
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Fernando Martínez Sáez
Medically reviewed by our Medical staff

Last update: 29-06-2021

How else can it be called?

  • Crystalluria

  • Oxalate crystals

  • Urate crystals

  • Phosphate crystals

  • ICD-10: R82.79

Why crystals can be present in urine?

Crystals are formed from the dissolved substances (especially salts) present in the urine.

Crystals frequently found in the urine has usually no diagnosis meaning. They may have a geometrical or an amorphous shape. The main reason for the identification of urinary crystals in the urine is to detect the presence of the relatively few abnormal types that may represent liver diseases, metabolism disorders or renal damage.

Salts precipitate more readily at low temperatures. Therefore, the majority of crystal formation takes place in samples remained at room temperature or that have been previously refrigerated.

The precipitation of these dissolved substances into crystals is affected by:

  • Temperature: Urine that has been at room temperature or refrigerated for a period of time will often contain abundant crystals in the urine sediment.
  • Specific gravity: Highly concentrated urine (urine with a high specific gravity) with many dissolved substances will crystallize readily.
  • pH of the urine: The pH of the urine specimen plays a valuable role when attempting to identify crystals under the microscope, as certain types of crystals are evident in acidic urine, whereas others are present in alkaline urine.

Why is this test performed?

Most crystals have little clinical significance because the presence of certain types of crystals in the urine is common.

It may be relevant when the presence of specific abnormal types of crystals (cystine, cholesterol, leucine, tyrosine, etc.) is detected and that may be a sign of metabolic or liver disorders.

Crystal in the urine may also appear in people under treatment with drugs such as sulfonamide or ampicillin.

How is the test performed?

This test is performed in the urine sediment examination. To study the crystals under the microscope, it is necessary to obtain previously the urinary sediment. For this matter, the urine sample should be placed at rest for some hours waiting for the different elements of the urine (white and red blood cells, epithelial cells, crystals, etc.) precipitate to the bottom. As this process is very slow, the urine is centrifuged for about 5 minutes at 1500 or 2000 revolutions per second to obtain a sample of the sediment in less time.

Once the sample has been studied under the microscope, the presence of abnormal crystals or normal crystals in increased amount is reported.

Common crystals in the urine

The presence of crystals in normal urine sediment is common. Although many types of crystals are considered normal, it is important to report them when identified because their presence in increased number may be clinically significant. Crystals are usually reported as rare, few, moderate, or many per HPF (High Power Field).

Normal crystals may be present in acidic or alkaline urine specimens with no clinical meaning. These include the following:

  • Acidic urine (pH <7):
    • Amorphous urates: They are present in acidic urine. Refrigeration of the urine sample contributes to the formation of amorphous urates. The urine sediment color is usually pink. Under the microscope, the amorphous crystals will appear as yellow-brown diffuse granules. They may appear when a person has a fever.
    • Uric acid: They are present in acidic urine. Uric acid crystals have a yellow or red-brown color. They have numerous shapes, although they often have a rhomboid shape. They may be present in increased numbers in patients with leukemia receiving chemotherapy, patients with Lesch-Nyhan syndrome and occasionally in patients with gout.
    • Calcium oxalate: They are found occasionally in acidic urine and more often with neutral urine. These crystals, under the microscope, have the shape of octahedral envelope and are very refractive. They may be present in increased numbers in case of diabetes mellitus, liver disorders or lithiasis (formation of calculi).
  • Alkaline urine (pH >7):
    • Amorphous phosphates: They are present in alkaline urine, especially after refrigeration of the sample. The urine sample may take on a white color if amorphous phosphates are present.
    • Triple phosphate (phosphate-ammonium-magnesium or struvite): They are present in neutral or alkaline urine. They are colorless, and very refractive under the microscope. They have a shape of three to six-sided prisms often described as a “coffin lid” or “fern-leaf”. In increased number it may be a sign of urinary tract infection.
    • Ammonium biurate: Yellow brown spheres “thorn apple”.
    • Calcium phosphate: They have a shape of stellate prisms. They appear in increased number in people with urinary tract obstruction or with a urinary catheter.
    • Calcium carbonate: Tiny colorless spheres or dumb-bells. In increased number may be related to a vegetarian diet or urinary tract infection.

Abnormal or pathological crystals in the urine

The presence of the following crystals in the urine sediment is always considered abnormal and may be indicative of metabolic diseases. Abnormal crystals must be always reported. Abnormal crystals are usually found in acidic urine and rarely in neutral urine:

  • Cystine: They are present in people suffering from cystinuria, a metabolic disorder that prevents reabsorption of cystine by the renal tubules. Cystine crystals are colorless, refractile and with hexagonal shape.
  • Cholesterol: They are not seen unless the urine sample has been previously refrigerated. They appear under the microscope as flat rectangles with notches out of the corners of the structure. Their presence is a sign of lipiduria (the presence of lipids in the urine) such as nephrotic syndrome.
  • Tyrosine: They look like yellow clumps of needles. They appear in case of liver disorders.
  • Leucine: They look like yellow-brown, oily spheres with radial and concentric striations. They appear also in case of liver disorders.
  • Bilirubin: They are seen as yellow lumps of needle structures. They suggest a liver disorder.
  • Hippuric acid: They are present in people exposed to toluene or xylene, two common industrial chemicals found in people who sniff glue product.

Which substances may interfere with the results?

The use of certain drugs such as sulfonamides (sulfadiazine), ampicillin or indinavir may also result in crystal formation of these substances in the urine.

Medically reviewed by our Medical staff on 29-06-2021


  • Laboratory tests and diagnostic procedures with nursing diagnoses (8th ed), Jane Vincent Corbett, Angela Denise Banks, ISBN: 978-0-13-237332-6, Pag. 75.
  • Essentials of Medical Laboratory Practice. Constance L. Lieseke, Elizabeth A. Zeibig. 2012. ISBN: 978-0-8036-1899-2 Pag: 444.
  • Concise Book of Medical Laboratory Technology: Methods and Interpretations. 2nd Edition. 2015. Ramnik Sood. ISBN: 978-93-5152-333-8. Pag. 99.
  • Urinalysis and Body Fluids. Susan King Strasinger. Marjorie Schaub Di Lorenzo. 5th edition. 2008. ISBN 978-0-8036-1697-4 Pag. 110.

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