Urine Analysis 

Sample Collection and Microscopic Examination

Urine analysis is the term used to refer to the test used to evaluate a urine sample. Typically, this test is used for the purposes of assessing a wide range of disorders, which may include kidney disease, urinary tract infection (UTI) dehydration as well as diabetes. The test will involve an examination of the appearance, concentration as well as content of the urine sample.

In microscopy, a sample of urine is centrifuged to obtain some sediment, which can then used to examine the presence of crystals, casts, white and/or red blood cells or bacteria/yeast infection. 

While the appearance or coloration can give some indication of the problem, microscopy allows for a deeper urine analysis, which would prove useful for diagnosis and prognosis.

Urine Analysis and Sample Collection 



For the purposes of microscopic urine analysis, the first morning specimen is the recommended specimen of choice. This due to the fact that it is generally more concentrated because of the amount of time it remained in the bladder.

As such, the sample would contain relatively higher amounts of such analytes as proteins or other cellular elements if at all they are present. To prevent any form of contamination, a midstream clean catch specimen is recommended.

Here, the patient/participant will be required to start by cleansing the urethral area using a castile soap towelette (or simply cleansed and rinsed well) A small amount of urine should then be voided in to the toilet in order to reduce the changes of contaminants from entering in to the collecting container before collecting the rest midstream in to the clean container.

Once the sample of urine has been properly collected:


  • Pour 10 to 15 ml of the well-mixed urine in to a test tube and place it in the centrifuge (the test tube should always be balanced with a second test tube filled with water/another urine sample) of equal volume
  • Centrifuge the sample at low speeds of between 2,000 to 3,000 rounds per minute for about 7 minutes,
  • Decant the supernate (to retain about 0.2- 0.5 ml inside the tube)
  • Shake the tube to mix the sediment and supernate retained in the test tube,
  • Using a pipette, collect and place a drop of the re-suspended sediment on to a microscopic slide and place a cover slip over the drop for observation,


Note** If the urine sample is not analyzed within 2 hours after collection, it should be stored for not more than 24 hours (refrigeration).

On the other hand, such chemicals as boric acid and tartaric acid may be used for preservation purposes. This allows for the urine to be kept at room temperature, and still provide similar results as refrigerated urine.

Preservation is important in that it allows for a stable environment for the specimen while reducing the risks of bacterial overgrowth or decomposition.

Multiple white cells seen in the urine of a person with a urinary tract infection using a microscopyMultiple white cells present in the urine of person with a urinary tract infection using microscopy By Bobjgalindo - Own work, GFDL, https://commons.wikimedia.org/w/index.php?curid=5652287

Microscopic Examination

For urine analysis, the sediment should first be observed under low power when observing for crystals, casts, squamous cells or other larger objects. When making a report, the number of casts seen under the microscope is usually reported as the number of each type per low power field. Moreover, low power allows for a wider view, which allows for clear observation of the number of casts seen.

To observe and identify cells, crystals and bacteria, high power is used. In this case, the types of cells will also be described as the number of each type found per the high power field.


Note** - When observing the slide under low power, low light source should be used. This is because of the fact that too much light would make it more difficult to see he cellular and crystalline elements. 


Typically, early morning sample before the ingestion of a liquid is preferred since it reflects the ability of the kidney to concentrate urine during dehydration, over a period of about 8 hours (during sleep).

On the other hand, random collection may be taken at a given time of the day without precaution with regards to contamination. Such samples may be isotonic, dilute, containing white cells or even bacteria among others.

During collection, voiding first half of the urine is recommended in order to flush out any possible contaminants (cells or microbes) which may still be present on the outer of the urethra. It therefore makes the urine analysis easier by eliminating any contaminants that may lead poor diagnosis and prognosis.

In this case, therefore, the technician only gets to observe and analyze the contents of the uncontaminated urine.  

Depending on the urine as well as how it was collected, the microscopic examination of the sediment may detect the presence of the following:

  • Red blood cells - Except in certain situations like during menstruation among women, no red blood cells should be present in a urine sample.
  • White blood cells - The presence of white blood cells in urine is indicative of an infection.
  • Epithelial cells - These cells normally slough in to the urine and can be seen in a urine sample. They include transitional and squamous epithelial cells.
  • Casts - Cylindrical structures produced in the kidney. They are present in urine in certain disease states.
  • Bacteria - Bacteria are common in urine. However, the significant numbers may be indicative of an infection.
  • Yeast - Yeast may either be contaminants or representative of true yeast infection.
  • Crystals - Crystals can be seen even in urine from a healthy person. They include triple phosphate crystals, calcium oxalate and amorphous phosphates.



Urine is a bio-fluid, which means that it is a fluid that originates from inside the body. As such; it should be handled with care. While care should be taken while collecting a urine sample to avoid contaminating it, it should also be handled with care while examining. This is a safety precaution that should involve the use of latex gloves.

Moreover, all the remaining fluids should be discarded safely. Although urine samples are not considered biohazard under the OSHA regulations/standards, it should be safely discarded in the laboratory sink and washed away with water.

While this experiment is easy with a lot to show, inexperienced students should be supervised to get the best results possible.

Related: Hematuria - Micrscopy of Urine and Observations, Microscopy Culture and Sensitivity

More on Leukocytes here

Of Interest: Sputum Microscopy, Blood Microscopy

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