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Microscopic Urinalysis is a crucial component of a urinalysis, a diagnostic test used to assess the health and function of the urinary system. This part of the test involves the examination of urine sediment under a microscope to identify and quantify various elements and cells present.

Purpose of Microscopic Urinalysis

Microscopic Urinalysis helps healthcare professionals detect and analyze various substances and particles in urine, including red and white blood cells, epithelial cells, casts, crystals, and bacteria. It provides valuable insights into the patient’s kidney and urinary tract health.

Collection and Preparation

Collecting a urine sample for diagnostic testing, such as urinalysis, is a straightforward process that requires careful handling to ensure accurate results. The urine sample is usually centrifuged to concentrate the sediment at the bottom of the tube. A small amount of the sediment is then placed on a glass slide and examined under a microscope.

Light Microscopy

Light microscopy of urine is a laboratory technique that involves the examination of urine sediment under a microscope to assess the health and function of the urinary system. This procedure is a critical part of urinalysis and provides valuable insights into a patient’s health. Light microscopy of urine is performed to identify and quantify various components and particles present in urine sediment. This analysis helps healthcare professionals diagnose and monitor a wide range of conditions related to the urinary system, kidney function, and overall health.

This procedure involves the examination of urine under a light microscope to identify a range of components, including ova or parasites (e.g., Trichomonas, Schistosoma, Echinococcosis, Filaria larvae), red blood cells (RBCs), white blood cells (leukocytes), casts, epithelial cells, and crystals. Additionally, it can reveal the presence of bacteria, yeast, cylindroids, spermatozoa, mucus, fat, and artifacts.

Preparation of Deposits

To prepare the sediment for examination, centrifuge a 10-15 ml well-mixed urine sample at 1000 rpm for 3 minutes. Carefully remove the supernatant and mix the sediment with a small amount of residual urine. Place a drop of the sediment on a clean glass slide, cover it with a cover slip, and examine it under subdued light. Start by scanning the entire area with the low-power objective, followed by the high-power objective. If amorphous deposits obscure important structures, add a small drop of 10% acetic acid to dissolve them, but be cautious not to use excessive acid to prevent cast dissolution. The elements to be noted under low power include casts, spermatozoa, mucous threads, yeast, fat droplets, and ova of parasites. Casts are reported in terms of the number per low-power field, while other elements are described as few, moderate, or many.


Normal urine from males should not contain more than 1 leukocyte per high-power field (HPF), whereas urine from females may contain 1-5 cells/HPF. Elevated leukocyte count (pyuria) typically signifies inflammation and can be observed in most renal diseases. Leukocyte casts are present in cases of renal infections. Some causes of pyuria include acute or chronic pyelonephritis, acute or chronic cystitis, renal tuberculosis, and bladder trauma. It’s essential to examine urine promptly after collection, as leukocytes may be lost in hypotonic alkaline urine over time.



Red blood cells (RBCs) appear as highly refractive, round, yellowish structures. Normal urine from males should not contain RBCs unless collected by catheterization. In females, a few RBCs may be present due to vaginal contamination, while menstruation can result in a higher count. Hematuria, the presence of RBCs in the urine, is a significant finding and can originate from various parts of the urinary system. Renal hematuria is characterized by the presence of RBCs, red-cell casts, proteinuria, and dysmorphic RBCs, with causes including glomerulonephritis, lupus nephritis, calculi, tumors, trauma, and acute infections. Hematuria of lower urinary tract origin lacks casts and protein, with causes like infection, calculi, bladder tumors, and urethral strictures.


Epithelial Cells

Squamous epithelial cells are normally present in small numbers, but a significant increase in females may indicate vaginal contamination. Tubular epithelial cells are associated with renal disease and resemble leukocytes but have a prominent nucleolus centrally located. These cells may contain bilirubin or hemosiderin.

Epithelial Cells
Epithelial Cells

Amorphous Deposits

In Microscopic Urinalysis, Amorphous deposits in urine are non-crystalline, shapeless substances that can be observed when examining a urine sample under a microscope. These deposits can vary in composition, color, and appearance. Here are some common types of amorphous deposits found in urine:

1. Amorphous Phosphates:

These deposits consist of salts of phosphate, such as calcium phosphate. They often appear as white or cloudy particles in the urine and are more likely to form in alkaline or basic urine conditions.

2. Amorphous Urates:

These deposits are primarily composed of uric acid or its salts, such as ammonium urate or sodium urate. They can appear as yellow or reddish-brown granules or sediments in the urine and are more likely to form in acidic urine conditions.

3. Amorphous Uric Acid:

In addition to urates, amorphous uric acid deposits can also occur in urine. They are typically colorless or pale yellow and can be seen in acidic urine conditions.

4. Amorphous Calcium Carbonate:

These deposits consist of calcium carbonate and can appear as small white particles in the urine sediment. They are usually seen in alkaline or basic urine.

5. Amorphous Cystine:

Amorphous cystine deposits are less common and are associated with the presence of the amino acid cystine. These can be seen in individuals with a rare genetic condition called cystinuria, which leads to the excessive excretion of cystine in the urine.

6. Amorphous Cholesterol:

These deposits contain cholesterol and can indicate underlying kidney or metabolic issues. They are relatively rare.

7. Amorphous Lipids:

Amorphous lipid deposits contain lipids or fats and can be found in the urine of individuals with conditions like nephrotic syndrome, where there is excessive loss of proteins in the urine.

8. Mixed Amorphous Deposits:

In some cases, amorphous deposits may contain a mixture of different substances, making them more challenging to identify and interpret.

Amorphous Deposits
Amorphous Deposits

The clinical significance of these amorphous deposits can vary depending on their composition, quantity, and the individual’s overall health and medical history. While small amounts of some amorphous deposits may be considered normal, larger amounts or specific types may suggest underlying medical conditions, dietary factors, or urinary pH imbalances.


In Microscopic Urinalysis, Casts in urine are cylindrical structures that can be observed under a microscope when examining a urine sample. They are formed in the renal tubules of the kidneys and are composed of proteins and other materials that have been precipitated and molded into a tubular shape. The presence of casts in urine can provide valuable information about kidney function and potential underlying medical conditions. Here are the main types of casts found in urine, along with some details about each:

1. Hyaline Casts:

These are the most common type of casts found in urine. They are transparent and colorless, and they consist mainly of a protein called Tamm-Horsfall protein, which is produced by the renal tubules. The presence of hyaline casts can be normal or indicate mild dehydration, stress, or exercise.

2. Granular Casts:

Granular casts are divided into two subtypes:

      • Fine Granular Casts: These casts are made up of finely granulated material and can be indicative of kidney injury, such as acute tubular necrosis.
      • Coarse Granular Casts: These are coarser and can be a sign of more severe kidney damage.

3. Cellular Casts:

These casts contain renal epithelial cells, red blood cells, white blood cells, or both. The presence of cellular casts may suggest kidney inflammation or injury, urinary tract infections, or glomerulonephritis.

4. Fatty Casts:

Fatty casts contain lipid (fat) droplets and are often seen in individuals with nephrotic syndrome, a kidney disorder associated with excessive loss of protein in the urine.

5. Waxy Casts:

Waxy casts are broad, have a waxy appearance, and typically indicate chronic kidney disease or severe kidney damage.

6. Red Blood Cell Casts:

These casts contain clumps of red blood cells and are usually indicative of bleeding in the nephrons. They can be associated with conditions such as glomerulonephritis or kidney inflammation.

7. White Blood Cell Casts:

These casts are made up of clumps of white blood cells and are typically a sign of inflammation or infection within the kidney or the urinary tract.

8. Crystalline Casts:

Crystalline casts are composed of crystals and may form in the renal tubules when there is an excess of certain substances in the urine, such as calcium, oxalate, or uric acid.

9. Mucus Casts:

Mucus casts contain mucus and are often seen in individuals with chronic kidney disease. They can be associated with excessive mucus production in the nephrons.

Typesof Casts
Types of Casts


In Microscopic Urinalysis, Crystals in urine are solid structures formed from minerals and other substances found in the urinary tract. They can vary in composition, shape, and clinical significance. Here are some common types of crystals found in urine, along with details about each:

1. Calcium Oxalate Crystals:

    • Composition: These crystals are primarily composed of calcium oxalate, a salt that can be found naturally in many foods.
    • Appearance: They often appear as colorless or pale yellow crystals with various shapes, including octahedrons, dumbbells, or envelope-like forms.
    • Clinical Significance: Calcium oxalate crystals can be normal in small amounts but may be associated with kidney stones when present in larger quantities.
Calcium Oxalate Crystals
Calcium Oxalate Crystals


2. Triple Phosphate Crystals (Struvite Crystals):

      • Composition: These crystals are made up of magnesium, ammonium, and phosphate. They are often associated with urinary tract infections caused by certain bacteria.
      • Appearance: Triple phosphate crystals are typically large, prism-like crystals with a coffin-lid appearance.
      • Clinical Significance: Their presence may indicate the presence of urease-producing bacteria and the potential for urinary tract stones (struvite or infection stones).


        Triple Phosphate Crystals (Struvite Crystals)
        Triple Phosphate Crystals (Struvite Crystals)

3. Uric Acid Crystals:

    • Composition: Uric acid crystals consist of uric acid, which is a byproduct of the breakdown of purines.
    • Appearance: They appear as yellow to reddish-brown crystals and can have various shapes, including rhomboids or needle-like crystals.
    • Clinical Significance: Uric acid crystals may be associated with conditions like gout or hyperuricemia, which can lead to uric acid kidney stones.


      Uric Acid Crystals
      Uric Acid Crystals

4. Cystine Crystals:

    • Composition: These crystals are composed of cystine, an amino acid. They are relatively rare and associated with a genetic disorder called cystinuria.
    • Appearance: Cystine crystals are hexagonal and appear colorless.
    • Clinical Significance: The presence of cystine crystals suggests a genetic disorder that leads to the excessive excretion of cystine in the urine, potentially leading to cystine kidney stones.


      Cystine Crystals
      Cystine Crystals

5. Ammonium Urate Crystals:

    • Composition: Ammonium urate crystals consist of ammonium and urate ions.
    • Appearance: They appear as yellow-brown, irregularly shaped crystals.
    • Clinical Significance: Ammonium urate crystals are associated with liver disease and can be found in urine samples from patients with liver disorders.


      Ammonium Urate Crystals
      Ammonium Urate Crystals

6. Bilirubin Crystals:

    • Composition: Bilirubin crystals are formed from bilirubin, a product of hemoglobin breakdown.
    • Appearance: They typically appear as yellow-brown or brown needles.
    • Clinical Significance: Bilirubin crystals in urine can indicate liver dysfunction or hemolysis (breakdown of red blood cells).


      Bilirubin Crystals
      Bilirubin Crystals

7. Cholesterol Crystals:

    • Composition: Cholesterol crystals are composed of cholesterol molecules.
    • Appearance: They can vary in shape but are often seen as colorless, flat, and rectangular plates.
    • Clinical Significance: The presence of cholesterol crystals can be associated with kidney disorders or metabolic abnormalities.


      Cholesterol Crystals
      Cholesterol Crystals

8. Tyrosine Crystals:

    • Composition: Tyrosine crystals are formed from the amino acid tyrosine.
    • Appearance: They appear as fine, colorless, needle-like crystals.
    • Clinical Significance: Tyrosine crystals can be found in conditions like tyrosinemia, a rare metabolic disorder.


      Tyrosine Crystals
      Tyrosine Crystals

9. Sulfonamide Crystals:

    • Composition: Sulfonamide crystals are related to the use of certain medications, sulfonamides, which can crystallize in the urine.
    • Appearance: These crystals may appear as thin, colorless needles or plates.
    • Clinical Significance: The presence of sulfonamide crystals in the urine is usually linked to the use of sulfonamide antibiotics and is generally not a cause for concern.


      Sulfonamide Crystals
      Sulfonamide Crystals

10. Leucine Crystals:

    • Composition: Leucine crystals are formed from the amino acid leucine.
    • Appearance: They appear as yellow or brown spheres with concentric rings.
    • Clinical Significance: Leucine crystals can be found in individuals with certain metabolic disorders, such as tyrosinemia or maple syrup urine disease.


      Leucine Crystals
      Leucine Crystals


In addition to the elements mentioned, the urinary sediment can contain various other components, including ova of parasites like Schistosoma haematobium, malignant cells, bacteria, yeast cells, trichomonas, filaria, mucous threads, and more. Dark-ground illumination may be necessary when specific organisms like Leptospira are suspected.

Automated Instrumentation

Automated equipment such as the Clinitek 100 and urilux has become increasingly popular for routine urine examination. These instruments reduce variability in visual interpretation, offer convenience and accuracy, support computer interfacing, and decrease the need for retesting. They contribute to more efficient and standardized urinalysis procedures.


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