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Nephrology · Renal

Nephrolithiasis

A stone is not just a stone. The crystal shape, urine pH, and imaging appearance together point to a different metabolic culprit and a different prevention strategy. Get the stone type wrong, and the patient keeps making new ones.

Match the Crystal to the Culprit

Four stone types, four distinct clue packages. Every board question buries the answer in one of them. Flip each card, then commit the pattern.

A 45-year-old man on a high-protein, low-fluid diet comes to the emergency department with acute, severe right flank pain radiating to the groin for the past 3 hours. He has gross hematuria. He has never had a stone before. Temperature is 37.0 C; he is writhing in distress and unable to find a comfortable position. Examination reveals right costovertebral angle tenderness. His urine pH is 5.1. Serum creatinine is 1.1 mg/dL. A plain abdominal X-ray shows no opacities over the urinary tract.
The X-ray shows nothing. What does that tell you about this stone, and what imaging should you get next?

There are four stone types that matter. Calcium oxalate accounts for about 80 percent of all stones. The other three each carry a board-specific clue set: struvite means urease, uric acid means radiolucent in acidic urine, and cystine means children with a transport defect. The clue in the stem tells you which world you are in. Flip each card.

Calcium OxalateTap to flip · Most common
The default stone
~80% of stones. Crystal shape: envelope or dumbbell. Radiopaque on X-ray (appears white). Forms in normal to acidic urine. Caused by hypocitraturia, malabsorption (Crohn disease), ethylene glycol, or excess vitamin C. Prevention: thiazide diuretic (reduces urinary calcium), potassium citrate (raises urine pH and citrate), high fluid intake.
StruviteTap to flip · Urease
Infection stone
Magnesium ammonium phosphate. Crystal shape: coffin-lid. Radiopaque. Grows into staghorn calculi filling the renal pelvis. Forms in alkaline urine (pH > 7.5) created by urease-producing bacteria: Proteus mirabilis, Klebsiella, or Pseudomonas. Urease splits urea into ammonia, which alkalinizes urine and precipitates the stone. You must treat the infection or the stone regrows.
Uric AcidTap to flip · Radiolucent
Invisible on X-ray
Radiolucent on plain X-ray (not visible on KUB). Crystal shape: rhomboid or needle-like. Forms in acidic urine (pH < 5.5). Associated with gout, high purine diets, myeloproliferative disorders, and Lesch-Nyhan syndrome. Treatment: alkalinize the urine with potassium citrate (goal pH 6.0–6.5), allopurinol to reduce uric acid production, reduce dietary purines.
CystineTap to flip · Children
Transport defect
Crystal shape: hexagonal. Mildly radiopaque. Forms in acidic urine. Caused by a defect in the amino acid transporter for COLA: Cystine, Ornithine, Lysine, and Arginine in the proximal tubule and gut. Autosomal recessive. Recurrent stones in children and young adults is the flag. The sodium cyanide-nitroprusside urine test turns red-purple with cystinuria. Treatment: high fluid intake, alkalinize urine, D-penicillamine or tiopronin if needed.
From the Attending The mnemonic the boards love for radiolucent stones: "I can't c (see) u (you)" stands for cystine and uric acid. Both are invisible on a plain X-ray. If a stem hands you a negative KUB with a classic stone presentation, your differential immediately narrows to those two. Then let urine pH and demographics sort it: acidic urine plus gout equals uric acid; hexagonal crystals plus a young patient equals cystine.

Pain, Blood, and the Blocked Kidney

The classic presentation is hard to miss. The dangerous complication is not. Post-renal oliguria from obstruction is the reason kidney stones matter beyond pain management.

The classic presentation is acute colicky flank pain. A stone leaving the kidney and entering the ureter generates severe, cramping pain starting in the flank and radiating downward toward the groin as the stone migrates. The pain is colicky because peristaltic waves periodically compress the stone, and ureteral spasm drives the cramping. The patient is usually writhing and cannot find a comfortable position, which is the opposite of the peritoneal pain patient who lies completely still.

Hematuria almost always accompanies the pain. The stone abrades the urothelium. Gross or microscopic hematuria is present in roughly 90 percent of stone episodes. Its absence does not exclude a stone, but its presence in a writhing patient with flank-to-groin pain is essentially a stone until proven otherwise.

No fever, no pyuria. An uncomplicated stone causes no infection and no systemic illness. Fever plus stone is an emergency: an obstructed, infected kidney is sepsis waiting to happen and needs urgent drainage, not just pain control.

Board Trap The post-renal oliguria vignette is the one that kills. A patient presents with acute flank-to-groin pain plus a sudden drop in urine output. The instinct is to think intrinsic renal failure, but the obstructing stone is the cause. Post-renal acute kidney injury from nephrolithiasis requires either bilateral ureteral obstruction or a stone in the solitary functioning kidney. The mechanism: back-pressure collapses the renal tubules and shuts down glomerular filtration. Workup is non-contrast CT. Not ultrasound, not urinalysis. Non-contrast CT.

Walk the obstruction chain once. Tap each step to reveal the beat.

A 58-year-old man on a high-protein, low-fluid diet develops acute right flank pain radiating to the groin plus his urine output drops from 1200 mL/day to 200 mL/day. What is the mechanism of the oliguria?
Right. The stone occludes the ureter. Hydrostatic pressure builds upstream in the collecting system and proximal tubule. When that pressure exceeds the driving pressure for filtration, GFR drops. This is post-renal AKI, fully reversible once the obstruction is relieved. The key: the BUN and creatinine rise, but the urine sediment is bland (no casts, no protein). Mechanical back-pressure, not tubular death.
The same patient has a plain abdominal X-ray that shows no stone. Can you exclude nephrolithiasis, or do you need more imaging?
Right. Plain X-ray misses uric acid and cystine stones entirely, and misses small calcium stones. Non-contrast CT detects virtually all stones and grades the hydronephrosis. This is the answer every time you are asked what workup to get for a suspected stone. Non-contrast CT, not KUB, not ultrasound (unless pregnant).
Non-contrast CT shows a 4 mm right ureteral stone with mild hydronephrosis and no signs of infection. The patient is in pain but tolerating oral fluids. Best management?
Right. Stones under 5 mm pass spontaneously in most patients. Alpha-blockers relax the ureteral smooth muscle and speed passage. Ketorolac is the analgesic of choice because it also reduces ureteral spasm. Intervention is reserved for stones greater than 10 mm, failure to pass after 4 to 6 weeks, infection, single kidney, or intractable pain. Under 5 mm: push fluids, relax the ureter, control pain, and wait.
From the Attending Know the intervention thresholds cold. Under 5 mm: watch and wait with an alpha-blocker. 5 to 10 mm: borderline; many pass but intervention is on the table. Over 10 mm: spontaneous passage unlikely; refer for ureteroscopy or extracorporeal shock wave lithotripsy. Staghorn calculus: percutaneous nephrolithotomy, because lithotripsy cannot handle that volume. Infected obstructed kidney at any size: urgent drainage first, stone second.

Which Stone Is This?

Answer four quick clinical questions and the tree lands you on a stone type with the full clue set. Run it until the logic is automatic.

Stone-Type Decision Tree
Tap the answer that fits the stem. The tree routes you to the stone and shows you why.
Is the stone visible on a plain abdominal X-ray (KUB)?
What is the urine pH?
Is there a history of recurrent urinary tract infections, or does the stone fill the renal pelvis in a branching pattern (staghorn)?
What is the patient profile?
Stone Type Identified
Calcium Oxalate
Most common stone (~80%). Radiopaque. Crystal shape: envelope or dumbbell. Urine pH normal to acidic. Causes: hypocitraturia, Crohn disease or other malabsorptive conditions, excess vitamin C, ethylene glycol ingestion. The boards also test calcium phosphate, which is radiopaque and forms in alkaline urine; if the context is distal renal tubular acidosis (type 1 RTA), think calcium phosphate stones in that alkaline, high-calcium milieu.

Prevention: thiazide diuretic (reduces urinary calcium), potassium citrate (raises urine pH and adds citrate, which chelates calcium and inhibits stone nucleation), adequate fluid intake (urine output > 2 L/day), moderate dietary calcium (low-calcium diets paradoxically increase oxalate absorption).
Stone Type Identified
Struvite (Magnesium Ammonium Phosphate)
Radiopaque. Crystal shape: coffin-lid. Forms in alkaline urine (pH > 7.5) from urease-producing bacteria. The mechanism chain: urease-positive bacteria (Proteus mirabilis, Klebsiella, Pseudomonas) hydrolyze urea → releases NH3 → urine pH rises above 7.5 → magnesium, ammonium, and phosphate precipitate together → stone grows rapidly and branches into the collecting system forming a staghorn calculus.

Prevention: eradicate the underlying infection. Acetohydroxamic acid can inhibit urease if infection cannot be cleared. These stones do not dissolve with pH manipulation; they require mechanical removal followed by definitive antibiotics.
Stone Type Identified
Uric Acid
Radiolucent on plain X-ray, but visible on CT (appears hyperdense on non-contrast CT). Crystal shape: rhomboid or needle-like. Urine pH < 5.5. Associated with gout, high-purine diets (red meat, organ meat, shellfish), myeloproliferative disorders with high cell turnover, and Lesch-Nyhan syndrome.

Prevention and treatment: alkalinize the urine with potassium citrate (goal urine pH 6.0 to 6.5), reduce dietary purines, allopurinol to reduce urate production. Unlike calcium stones, uric acid stones can dissolve with medical management (alkalinization alone can chemically dissolve existing stones).
Stone Type Identified
Cystine
Mildly radiopaque (less than calcium; may look faint on X-ray). Crystal shape: hexagonal. Urine pH acidic. Autosomal recessive defect in the COLA transporter (Cystine, Ornithine, Lysine, Arginine) in the proximal tubule and intestine. All four amino acids spill into the urine. Only cystine is insoluble enough to precipitate.

Detection: sodium cyanide-nitroprusside test turns brick-red with cystinuria. Prevention: very high fluid intake, alkalinize urine (cystine is more soluble at pH > 7.0), D-penicillamine or tiopronin (chelate cystine to form more soluble complexes) for refractory cases.

Quick-reference: stone types at a glance. The table locks in the comparisons the boards probe most.

Stone TypeCrystal ShapeRadiopacityUrine pHKey Association
Calcium oxalateEnvelope or dumbbellRadiopaqueAcidic to normalMost common; hypocitraturia, Crohn, vit C excess
StruviteCoffin-lidRadiopaqueAlkaline (>7.5)Urease bacteria; staghorn calculus
Uric acidRhomboid / needleRadiolucentAcidic (<5.5)Gout, high purines; dissolves with alkalinization
CystineHexagonalFaintly opaqueAcidicCOLA defect; children/young adults
Medically reviewed by Kaitlyn Cocuzzo, MD and Fatima Ali, DO · Last reviewed June 2026
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