Kidney Stones: Types, Crystals & Treatment for Step 1

Creator: Progress Note
Published: 2026-05-02
Keywords: kidney stones USMLE, kidney stones, nephrolithiasis, calcium oxalate stones, struvite staghorn, uric acid stones radiolucent, cystinuria hexagonal crystals, enteric hyperoxaluria, potassium citrate, thiazide stones, noncontrast ct kidney stone

bolt The 60-second version

check_circleCalcium oxalate is the most common stone; risk factors include idiopathic hypercalciuria, enteric hyperoxaluria (fat malabsorption, Crohn disease), low urine citrate, and ethylene glycol.
check_circleCalcium phosphate forms in alkaline urine: distal (type 1) RTA and primary hyperparathyroidism.
check_circleStruvite (magnesium ammonium phosphate): urease-producing bacteria (Proteus, Klebsiella) raise urine pH; staghorn calculi; "coffin-lid" crystals.
check_circleUric acid stones form in acidic urine (gout, tumor lysis, myeloproliferative disease); radiolucent on plain x-ray but visible on CT; treat by alkalinizing urine.
check_circleCystine: autosomal recessive defect in the proximal tubule transporter for cystine, ornithine, lysine, and arginine; hexagonal crystals; positive cyanide-nitroprusside test.
check_circleNoncontrast CT is the best imaging test (ultrasound in pregnancy and children); thiazides lower urine calcium, citrate raises urine pH and inhibits crystallization.

target What you'll be able to do · aligned to USMLE Step 1 · Renal

PATHIdentify the five main stone types by risk factors, urine pH, and crystal shape.
PHYSExplain enteric hyperoxaluria and urease-driven struvite formation.
RENALChoose imaging and acute management for nephrolithiasis.
PHARMDescribe preventive therapy, including thiazides, citrate, and allopurinol.

How kidney stones are tested on Step 1

Expect colicky flank pain radiating to the groin with hematuria, plus a crystal description, a urine pH, or an underlying disease.

Five stone types. Calcium stones together account for most stones.

Stone types compared

Urine pH, crystal shape, and radiographic density distinguish them.

Stone	Urine pH	Crystal shape	Plain x-ray	Prevention
Calcium oxalate	Any (often acidic)	Envelope (dihydrate) or dumbbell (monohydrate)	Radiopaque	Fluids, thiazide, citrate, low sodium, normal calcium intake
Calcium phosphate	Alkaline	Wedge-shaped prisms	Radiopaque	Fluids, thiazide; treat cause
Struvite	Alkaline	Coffin lid	Radiopaque	Eradicate infection; remove stone
Uric acid	Acidic	Rhomboid or rosettes	Radiolucent	Alkalinize urine (citrate), allopurinol
Cystine	Acidic	Hexagonal	Faintly radiopaque	Fluids, alkalinization, tiopronin or penicillamine

Restricting dietary calcium increases oxalate absorption and stone risk; normal calcium intake is advised.

Urine pH. Potassium citrate raises urine pH and also inhibits calcium crystal formation.

Mechanisms behind key stones

Several stones are tested through their underlying physiology.

Enteric hyperoxaluria: unabsorbed fatty acids bind calcium in the gut, leaving oxalate free to be absorbed in the colon (Crohn disease, bowel resection, bariatric surgery).
Struvite: urease splits urea into ammonia, which alkalinizes urine and supplies ammonium for magnesium ammonium phosphate.
Uric acid: uric acid is poorly soluble at low pH; a persistently acidic urine (as in gout or metabolic syndrome) promotes stones even with normal uric acid excretion.
Ethylene glycol: metabolized to oxalate, causing calcium oxalate crystals, AKI, and an anion gap acidosis.

Presentation and management

Most small stones pass; infection with obstruction is an emergency.

Acute management. Stones under about 5 mm usually pass; larger stones may need lithotripsy or ureteroscopy.

Worked example

Combine the clinical setting with urine findings.

functions Worked example — staghorn calculus

A woman with recurrent UTIs has a large branching stone filling the renal pelvis. Urine pH is 8.0 and microscopy shows coffin-lid crystals. What produces this stone?

Alkaline urine plus coffin-lid crystals = struvite.
Struvite needs urease-producing organisms (Proteus is classic).
Urease converts urea to ammonia, alkalinizing urine and providing ammonium.
The stone harbors bacteria, so it must be removed and the infection eradicated.

Answer. A urease-producing organism, classically Proteus mirabilis, causing a struvite staghorn calculus.

Next in the roadmap

Kidney Stones

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quiz Test yourself

Quick check — 3 questions

1. A patient with Crohn disease and ileal resection develops kidney stones. Which stone is most likely?

2. A child has recurrent stones with hexagonal crystals. Which amino acids are poorly reabsorbed?

3. Which treatment is most useful for uric acid stones?

Frequently asked questions

What is the most common type of kidney stone?expand_more

Calcium oxalate.

Which stones are radiolucent on plain x-ray?expand_more

Uric acid stones. They are visible on noncontrast CT.

Why do thiazides prevent calcium stones?expand_more

They increase calcium reabsorption in the distal tubule, lowering urine calcium.

Should patients with calcium stones restrict dietary calcium?expand_more

No. Low calcium intake increases intestinal oxalate absorption and stone risk. Normal calcium intake with reduced sodium is advised.

References & further reading

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