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Microscopic examination of urine sediment
Last reviewed: 07.07.2025

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Microscopic examination of urine sediment (sediment microscopy) is an integral and essential part of a general clinical examination. A distinction is made between elements of organized and unorganized urine sediment. The main elements of organized sediment include erythrocytes, leukocytes, epithelium and cylinders; unorganized sediment - crystalline and amorphous salts.
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Epithelium in urine
In healthy people, single cells of flat (urethra) and transitional epithelium (pelvis, ureter, urinary bladder) are found in the urine sediment. Renal (tubules) epithelium is absent in healthy people.
Squamous epithelium in urine
In men, only single cells are normally detected, their number increases with urethritis and prostatitis. In women's urine, squamous epithelial cells are present in greater quantities. The detection of strata of squamous epithelium and horny scales in the urine sediment is an unconditional confirmation of squamous cell metaplasia of the mucous membrane of the urinary tract.
- Transitional epithelial cells may be present in significant quantities in acute inflammatory processes in the urinary bladder and renal pelvis, intoxications, urolithiasis and neoplasms of the urinary tract.
- The cells of the epithelium of the urinary tubules (renal epithelium) appear in nephritis, intoxication, and circulatory failure.
In renal amyloidosis, renal epithelium is rarely detected in the albuminuric stage, and often in the edematous-hypertonic and azotemic stages. The appearance of epithelium with signs of fatty degeneration in amyloidosis indicates the addition of a lipoid component. The same epithelium is often detected in lipoid nephrosis. The appearance of renal epithelium in very large quantities is observed in necrotic nephrosis (for example, in poisoning with mercury chloride, antifreeze, dichloroethane, etc.).
Leukocytes in urine
Normally absent, or isolated ones are detected in the preparation and in the field of view. Leukocyturia (more than 5 leukocytes in the field of view or more than 2000/ml) can be infectious (bacterial inflammatory processes of the urinary tract) and aseptic (in glomerulonephritis, amyloidosis, chronic rejection of a renal transplant, chronic interstitial nephritis). Pyuria is considered to be the detection of 10 leukocytes in the field of view in the sediment obtained by centrifugation of urine or in 1 ml of non-centrifuged urine using high-resolution microscopy (×400).
Active leukocytes (Sternheimer-Malbin cells) are normally absent. "Live" neutrophils penetrate into the urine from the inflamed renal parenchyma or from the prostate. The detection of active leukocytes in the urine indicates an inflammatory process in the urinary system, but does not indicate its localization.
Red blood cells in urine
Normally, there are none in the urine sediment, or single ones in the preparation. If erythrocytes are detected in the urine, even in small quantities, further observation and repeated studies are always necessary. The most common causes of hematuria are acute and chronic glomerulonephritis, pyelitis, pyelocystitis, chronic renal failure, kidney injury, bladder injury, urolithiasis, papillomas, tumors, tuberculosis of the kidneys and urinary tract, overdose of anticoagulants, sulfonamides, urotropin.
Cylinders in urine
Normally, there may be hyaline casts (single in the preparation) in the urine sediment. Granular, waxy, epithelial, erythrocyte, leukocyte casts and cylindroids are normally absent. The presence of casts in the urine (cylindruria) is the first sign of a reaction from the kidneys to a general infection, intoxication or to the presence of changes in the kidneys themselves.
- Hyaline casts consist of protein that gets into the urine due to stagnation or inflammation. Even significant amounts of hyaline casts may appear in proteinuria that is not associated with kidney damage (orthostatic albuminuria, stagnant, associated with physical exertion, cooling). Hyaline casts often appear in febrile conditions. Hyaline casts are almost always found in various organic kidney damages, both acute and chronic. There is no parallelism between the severity of proteinuria and the number of casts (it depends on the pH of the urine).
- Epithelial cylinders are exfoliated and "glued" together epithelial cells of the tubules. The presence of epithelial cylinders indicates damage to the tubular apparatus. They appear in nephrosis, including, as a rule, in significant quantities in nephronecrosis. The appearance of these cylinders in nephritis indicates the involvement of the tubular apparatus in the pathological process. The appearance of epithelial cylinders in urine always indicates a pathological process in the kidneys.
- Granular casts are composed of tubular epithelial cells and are formed when there is marked degeneration in the epithelial cells. The clinical significance of their detection is the same as that of epithelial casts.
- Waxy casts are found in severe lesions of the renal parenchyma. They are most often detected in chronic kidney diseases (although they can also appear in acute lesions).
- Red blood cell casts are formed from clusters of red blood cells. Their presence indicates a renal origin of hematuria (found in 50-80% of patients with acute glomerulonephritis). It should be borne in mind that red blood cell casts are observed not only in inflammatory kidney diseases, but also in renal parenchymatous hemorrhages.
- Leukocyte casts are observed quite rarely, almost exclusively in pyelonephritis.
- Cylindroids are mucus threads originating from the collecting ducts. They often appear in the urine at the end of the nephritic process and have no diagnostic value.
Salts and other elements
The precipitation of salts depends mainly on the properties of urine, in particular on its pH. Uric and hippuric acid, urate salts, calcium phosphate, calcium sulfate precipitate in urine that has an acidic reaction. Amorphous phosphates, triple phosphates, neutral magnesium phosphate, calcium carbonate, and sulfonamide crystals precipitate in urine that has an alkaline reaction.
- Uric acid. Uric acid crystals are normally absent. Early (within 1 hour after urination) precipitation of uric acid crystals indicates a pathologically acidic pH of the urine, which is observed in renal failure. Uric acid crystals are found in fever, conditions accompanied by increased tissue breakdown (leukemia, massive decaying tumors, resolving pneumonia), as well as in heavy physical exertion, uric acid diathesis, and consumption of exclusively meat foods. In gout, significant precipitation of uric acid crystals in the urine is not observed.
- Amorphous urates are uric acid salts that give the urine sediment a brick-pink color. Amorphous urates are normally single in the field of vision. They appear in large quantities in the urine in acute and chronic glomerulonephritis, chronic renal failure, congestive kidney, and febrile conditions.
- Oxalates are salts of oxalic acid, mainly calcium oxalate. Normally, oxalates are single in the field of vision. They are found in significant quantities in urine in pyelonephritis, diabetes mellitus, calcium metabolism disorders, after an epileptic seizure, and when consuming large amounts of fruits and vegetables.
- Triple phosphates, neutral phosphates, calcium carbonate are normally absent. They appear during cystitis, abundant intake of plant foods, mineral water, vomiting. These salts can cause the formation of stones - more often in the kidneys, less often in the bladder.
- Acidic ammonium urate is normally absent. It appears in cystitis with ammonia fermentation in the bladder; in newborns and infants in neutral or acidic urine; uric acid infarction of the kidneys in newborns.
- Cystine crystals are normally absent; they appear in cystinosis (a congenital disorder of amino acid metabolism).
- Crystals of leucine and tyrosine are normally absent; they appear in acute yellow liver dystrophy, leukemia, smallpox, and phosphorus poisoning.
- Cholesterol crystals are normally absent; they are found in amyloid and lipoid dystrophy of the kidneys, echinococcosis of the urinary tract, neoplasms, and kidney abscesses.
- Fatty acids are normally absent; they are rarely detected in fatty degeneration and the breakdown of the epithelium of the renal tubules.
- Hemosiderin (a breakdown product of hemoglobin) is normally absent; it appears in the urine in hemolytic anemia with intravascular hemolysis.
- Hematoidin (a breakdown product of hemoglobin that does not contain iron) is normally absent, but appears in calculous pyelitis, renal abscess, and neoplasms of the bladder and kidneys.
Bacteria, fungi and protozoa in urine
Bacteria are normally absent or their number does not exceed 2×10 3 in 1 ml. Bacteriuria is not an absolutely reliable evidence of an inflammatory process in the urinary system. The content of microorganisms is of decisive importance. The presence of 10 5 microbial bodies or more in 1 ml of urine of an adult can be regarded as an indirect sign of an inflammatory process in the urinary organs. Determination of the number of microbial bodies is performed in a bacteriological laboratory; when studying a general urine analysis, only the fact of the presence of bacteriuria is stated.
Yeast fungi are normally absent; they are detected during glucosuria, antibacterial therapy, and long-term storage of urine.
Protozoa are normally absent; Trichomonas vaginalis is often detected in urine tests.
Sperm in urine
What does sperm in urine indicate and why does it appear there? This phenomenon is quite common. It is called retrograde ejaculation. In normal cases, sperm comes out through the urine outlet. The main symptom of this disease is the absence of sperm ejection through the urethra. Retrograde ejaculation can also be expressed in the complete absence of sperm.
If after orgasm it gets into the bladder, then during urination the man may notice cloudy urine. If you do a urine test in the laboratory, you can detect the presence of sperm in it.
When the penis is erect, the sphincter contracts and thus prevents urine and sperm from mixing. If the sphincter is too weak, sperm can penetrate into the urine. It is necessary to resolve this issue with the attending physician. The problem is not really serious, but nevertheless, it requires a timely solution. But first, it is necessary to diagnose the problem. After all, sperm in the urine is not a very good state of affairs.