Urine microscopy revealing a metabolic disorder: a case report

BACKGROUND: Primary hyperoxaluria type 3 is a rare autosomal recessive disorder caused by HOGA1 mutations, leading to recurrent calcium oxalate nephrolithiasis. Diagnosis is often delayed, and 24-hour urine oxalate measurements can be unreliable in patients with normal kidney function. Urine microscopy can detect high-density calcium oxalate monohydrate crystals, providing a rapid diagnostic clue. CASE PRESENTATION: A 31-year-old woman with recurrent nephrolithiasis since age 9 had undergone prior percutaneous nephrolithotomy and ureteroscopy. Urine microscopy revealed abundant calcium oxalate monohydrate crystals (280/mm³), and stone analysis showed mixed calcium phosphate, calcium oxalate dihydrate and monohydrate. Genetic testing confirmed homozygous HOGA1 mutation (c.700 + 5G > T). Conservative management with hydration, dietary calcium, and potassium citrate normalized citrate but not crystalluria. Adjunctive phytate therapy led to disappearance of calcium oxalate monohydrate crystals within weeks. Renal function and residual stones remained stable over 24 months. CONCLUSION: Detection of > 200 calcium oxalate monohydratecrystals/mm³ is highly suggestive of primary oxaluria type 3. Urine microscopy is rapid, inexpensive, and complements genetic testing. Conservative therapy remains central, and adjunctive measures like phytate may help reduce crystallization risk.