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Urine crystals

14 min

Skills you'll build2 skills
  • Identify common urine crystals by shape, urine pH, color, and birefringence
  • Recognize colorless hexagonal crystals that need a cystine confirmation test

At the bench: Identify and report cells, casts, crystals, and other urine sediment findings

Try first

Try first

A urine was refrigerated overnight. Its pH is 5.5, and it has a heavy pink sediment of fine granules. What is the precipitate most likely to be?

Keep going to see the reasoning.

Keep going to see the reasoning.

Keep going to see the reasoning.

Right. Keep going to follow the reasoning.

Keep going to see the reasoning.

Get the idea

Use the explanation to check your first decision.

Identifying a crystal in the sediment

A crystal forms when a substance exceeds its solubility. Urine pH, concentration, temperature and storage all change that. Cooling in the refrigerator precipitates urates and phosphates that were dissolved at body temperature. Several crystals share a shape, so the pH, the color, polarized light and solubility are used together to identify them.1,3

CrystalUsual pHAppearance in the sedimentCheck that confirms it
Amorphous uratesAcidicYellow-brown granules, pink sedimentDissolve with gentle warming
Uric acidAcidicYellow-brown rhomboids, wedges, rosettesStrong birefringence
Calcium oxalate dihydrateAcidic to neutralColorless envelopesSharp outline, birefringent
Calcium oxalate monohydrateAcidic to neutralColorless ovals or dumbbellsMany of them need urgent clinical correlation
Amorphous phosphatesNeutral to alkalineColorless granules, white sedimentDissolve in dilute acetic acid
Triple phosphateAlkalineColorless prisms like coffin lidsShape in alkaline urine
CystineAcidicColorless hexagonal platesAmino acid analysis or another validated test

Solubility tests go on a separate portion so the sediment stays intact for the count.3 Abundant calcium oxalate monohydrate can accompany ethylene glycol exposure, so it is reported promptly under the laboratory's procedure.1,2

Cystine and uric acid hexagons

Cystine forms colorless, flat hexagonal plates in acidic urine. It supports cystinuria, an inherited defect in the tubular reabsorption of cystine and the dibasic amino acids. Cystinuria causes recurrent stones, often starting in childhood or young adulthood.4

Uric acid can also form hexagons. Uric acid is usually yellow to brown, polarizes strongly and appears with its other shapes in the same field.1,3 Colorless hexagons are reported as the procedure directs and sent for confirmation by amino acid analysis or another validated method.1,4 A crystal's shape and color suggest its identity. Finding one rarely establishes a disease.1

Follow the bench demonstration

Sources for this step
References
  1. Kouri TT, Hofmann W, Falbo R, et al. The EFLM European urinalysis guideline 2023. Clin Chem Lab Med. 2024;62(9):1653-1786. doi:10.1515/cclm-2024-0070
  2. Cavanaugh C, Perazella MA. Urine sediment examination in the diagnosis and management of kidney disease: Core Curriculum 2019. Am J Kidney Dis. 2019;73(2):258-272. doi:10.1053/j.ajkd.2018.07.012
  3. Strasinger SK, Di Lorenzo MS. Urinalysis and Body Fluids. 7th ed. F.A. Davis; 2021. ISBN 978-0-8036-7582-7. F.A. Davis catalog record.
  4. Spasiano A, Halbritter J, Ferraro PM. Cystinuria. In: Adam MP, Bick S, Mirzaa GM, et al, eds. GeneReviews. University of Washington, Seattle; 1993-2026. Published November 20, 2025. Cystinuria. Accessed September 27, 2026.

Watch one

Read each decision and its explanation.

A urine from a 16-year-old with a second kidney stone this year has pH 6.0. At high power you see flat colorless plates with six sides, some stacked on each other. What do you report?

  1. Check the pH first: 6.0 is acidic and fits either.

    Both cystine and uric acid crystallize in acidic urine, so the pH narrows the list to these two.

  2. Look at the color: the plates are colorless.

    Uric acid is usually tinted yellow to brown, and cystine is colorless.

  3. Scan the rest of the field: there are no rhomboids, wedges or rosettes.

    Uric acid usually shows several shapes in the same field.

  4. Read the requisition: a second stone in a teenager makes the finding more significant.

    The history of repeat stones in a young person fits cystinuria.

  5. Report the hexagonal crystals and request the confirmation test the procedure specifies.

    Shape does not confirm cystine, and the confirmation follows the procedure.

Report colorless hexagonal crystals consistent with cystine, and send the specimen for confirmation by amino acid analysis or another validated method.

Practice this skill

Your turn

Problem 1 of 3 · Hints available

Point to the crystals that need a confirmation test for an inherited disorder of amino acid transport.

Four unlabeled urine sediment photomicrographs in two rows of two.

Image sources and licenses

  1. Top left
  2. Top right
  3. Bottom left
  4. Bottom right
Hint
  1. The disorder causes repeated kidney stones in young people.
  2. Count the sides of each crystal.
Show the answer

Cystine

Cystine forms colorless hexagonal plates and supports cystinuria. It is confirmed by amino acid analysis or another validated method. Oxalate and triple phosphate are common salts, and starch is an artifact.

Review Clinically significant and drug-associated crystals

Problem 2 of 3 · Hints available

A urine with pH 8.0 contains one of these crystal types. Point to the one that fits its pH.

Three unlabeled urine sediment photomicrographs, two above and one below.

Image sources and licenses

  1. Top left
  2. Top right
  3. Bottom
Hint
  1. Group the crystals by the pH each one forms in.
  2. Urease-producing bacteria raise the pH and help this crystal form.
Show the answer

Triple phosphate

Triple phosphate forms colorless coffin-lid prisms in alkaline urine. Calcium oxalate forms in acidic to neutral urine, and cystine in acidic urine.

Review Common crystals

Problem 3 of 3 · On your own

A refrigerated urine with pH 7.5 has a white precipitate of colorless granules. Gentle warming leaves it unchanged. A drop of dilute acetic acid on a separate portion clears it. What is the precipitate?

Urates form in acidic urine, give a pink or yellow-brown sediment and dissolve with warming. This precipitate matches none of the three.

Named a crystal from its shape alone

Urine pH, color, birefringence, and solubility separate crystals that share shapes. Amorphous urates form in acidic urine and amorphous phosphates in alkaline urine, and hexagonal uric acid can mimic cystine. Naming a crystal from shape alone can misidentify it and misdirect follow-up.

Calcium oxalate forms distinct colorless envelopes. It does not form a white granular precipitate that clears in acetic acid.

Colorless granules in alkaline urine, a white precipitate, and clearing in dilute acetic acid all fit amorphous phosphates.

Bacteria do not dissolve in dilute acetic acid, and they do not form a white precipitate in the refrigerator.

Review Common crystals

Use it

Read the case evidence, then make each decision. The step is complete without it.

  • Talia Voss, 11, comes to the stone clinic after her second kidney stone. Her first-morning urine was refrigerated overnight before transport.
  • Strip: pH 5.5, specific gravity 1.025, blood 1+.
  • The sediment is coated with pink fine granules that obscure the field.
  • After gentle warming of a portion, the granules clear. Red cells 3 to 5/HPF and a few flat, colorless six-sided plates become visible.
  • The plates show no rhomboids or rosettes beside them.
Decision 1 of 2

What was the pink precipitate, and does it belong on the report as a significant finding?

Pink granules in cold acidic urine that clear on warming are urates. They formed during refrigeration and have no clinical significance.

Phosphates form in alkaline urine, leave a white sediment and do not clear on warming.

Named a crystal from its shape alone

Urine pH, color, birefringence, and solubility separate crystals that share shapes. Amorphous urates form in acidic urine and amorphous phosphates in alkaline urine, and hexagonal uric acid can mimic cystine. Naming a crystal from shape alone can misidentify it and misdirect follow-up.

Warming cleared the precipitate and the sediment can be read. Refrigeration is an accepted way to store a urine.

Review Common crystals

Decision 2 of 2

What do you do about the six-sided plates?

Uric acid is usually yellow-brown and appears with rhomboids and rosettes. These plates are colorless and are the only crystals present.

The rest of the urinalysis is valid now. The plates fit cystine, and the comment states that a confirmation test is pending.

Colorless hexagons in acidic urine from a child with repeat stones suggest cystinuria. Omitting them leaves out a finding that needs confirmation.

Dismissed colorless hexagonal plates as a routine salt

Colorless hexagonal plates in acidic urine suggest cystine, which supports cystinuria, although hexagonal uric acid can look similar. Dismissing them as a routine crystal misses a finding that needs amino acid analysis or another confirmatory test.

A crystal suggests cystine. The disorder is established by confirmation testing and the clinical evaluation.

Review Clinically significant and drug-associated crystals

The key finding is colorless hexagons in acidic urine, visible once warming cleared the urates. Uric acid would show color and other shapes. The report names the crystals, with the confirmation pending.

For reference

Sources checked