Guide to Squamous Epithelial Cells in Urine

WRITTEN BY

The Levels Team

Updated: 05/22/2025|12 min read

Summary

Squamous epithelial cells form the outer layer of skin and line blood vessels and organs. When found in abnormal amounts in urine, they can indicate urinary tract inflammation, infection, or possible contamination during sample collection.

Why It Matters

Squamous epithelial cells make up the outermost layer of the skin and mucous membranes throughout the body, including parts of the urinary tract. In women, squamous epithelial cells line the urethra, vagina, and parts of the external genitalia, while in men, they're primarily found in the urethra.

These cells naturally shed, so finding a small number of them in urine is considered normal. However, elevated levels can suggest inflammation or infection in the lower urinary tract or genital regions. Conditions such as urethritis, vaginitis, or balanitis (inflammation of the head of the penis) can cause increased sloughing of squamous cells.

Because some squamous epithelial cells are normal in urine, providers need to distinguish between sample contamination and levels that indicate a potential condition. (Contamination happens when urine samples include cells from the skin, vagina, or external genitalia due to improper collection, such as not cleaning the genital area or failing to discard the initial urine stream. This is why "clean-catch" urine sample is generally emphasized.)

Associated Symptoms 

Squamous epithelial cells in urine themselves are a laboratory finding rather than a medical condition. However, elevated levels may be associated with various urinary and genital conditions, each with its own symptoms.

Common symptoms that may indicate conditions associated with high levels of squamous epithelial cells:

• Burning urination: Pain or discomfort during urination, potentially suggesting inflammation of the urethra or bladder
• Urinary frequency: Increased need to urinate can be related to irritation of the urinary tract
• Cloudy or odorous urine, or blood in urine: Changes in urine appearance or smell may be due to increased cells and possible infection
• Lower abdominal discomfort: Mild pain or pressure in the pelvic region, potentially resulting from inflammation
• Genital irritation: Itching, redness, or discomfort of the external genitalia that may contribute to increased cell shedding
• Abnormal discharge: Unusual vaginal or urethral secretions, potentially suggesting inflammation or infection

It's important to note that finding some squamous epithelial cells in urine is normal due to natural shedding. Elevated levels must be interpreted in the context of other findings and symptoms, as they may simply represent sample contamination during collection rather than a pathological condition. When squamous cells appear alongside white blood cells and bacteria, an infection may be the cause.

Clinical Ranges

Lab Reference Range: ≤5 /HPF

Lifestyle Factors That Can Impact It

Activities that may affect squamous epithelial cells in urine include:

• Hydration levels: Not drinking enough fluids concentrates urine, potentially irritating the urinary tract lining and increasing cell shedding.
• Holding urine for extended periods: Regularly delaying urination can stretch the bladder excessively and may irritate the epithelial lining.
• Personal hygiene: Poor hygiene practices can introduce bacteria to the urinary tract that increase squamous cell shedding. Proper wiping technique (front to back), regular cleaning, and wearing breathable underwear can help prevent bacterial growth.

Other Factors That Can Impact It

Medical Conditions

• Urinary tract infections (UTIs). Bacterial infections cause inflammation of the urinary tract lining, leading to increased cell shedding.
• Interstitial cystitis: This chronic condition involves inflammation of the bladder wall without infection, causing increased shedding of epithelial cells.  
• Vaginitis and vulvovaginitis: Inflammation of the vagina or vulva, from bacterial, fungal, or parasitic infections, increases the shedding of vaginal squamous cells that may contaminate urine samples.
• Squamous metaplasia of the bladder: A rare condition where the transitional epithelium of the bladder transforms into squamous epithelium in response to chronic irritation or inflammation, resulting in increased squamous cells in urine.
• Physical trauma or irritation: Mechanical injury from catheters, sexual activity, or irritants (soaps, spermicides, douches) can damage the urethral or vaginal epithelium, causing increased shedding of squamous cells into urine

Medications and Supplements

• Certain chemotherapy drugs
• Long-term use of indwelling catheters
• Radiation therapy to the pelvic region

Individual Factors

• Age: Postmenopausal women may have thinning urogenital tissue, affecting cell shedding.
• Sex: Women typically have higher levels of squamous cells in urine due to anatomical differences.
• Pregnancy: Hormonal changes may increase vaginal discharge and cell turnover.
• Menstruation: Can increase the presence of squamous cells in urine samples collected during this time.

Testing Accuracy and Stability

Squamous epithelial cell testing is generally reliable, but it can be affected by collection technique.

Factors That Can Affect the Accuracy of Your Test 

• Improper collection can affect levels
• Hydration
• Sample contamination with vaginal secretions or external genitalia cells

How It Relates to Other Markers

Other tests can provide insights about health status when they're viewed alongside squamous epithelial cell results. These tests may include:

• Urine culture: Identifies specific bacteria if infection is suspected.
• Pelvic examination: For women with persistent elevated squamous cells, a pelvic exam can identify vaginal or cervical conditions that might contribute to contamination of urine samples.
• Cystoscopy: Direct visualization of the bladder and urethra is usually considered only if symptoms persist after treatment or if other abnormalities (e.g., blood, atypical cells) are found.

What Results May Mean in the Context of Other Markers

• Squamous cells + white blood cells + bacteria: This combination can suggest a UTI.
• Squamous cells + red blood cells: May indicate non-infectious inflammation, stones, or possible tumors.
• Squamous cells + atypical cells: This requires careful evaluation for potential cancer.

Follow-up Considerations

If squamous epithelial cells in your urine is high, your provider may make some of the following recommendations. You should always speak to your doctor if you have medical questions or before making medical decisions.

When Re-Testing May Be Appropriate

• 2-4 weeks after any finding elevated levels
• As part of regular monitoring if you have recurrent urinary issues
• Following any changes in symptoms related to urination

Additional Testing Your Doctor May Consider

• Vaginosis tests if vaginal infection is suspected
• Imaging studies (ultrasound, CT) for persistent unexplained symptoms
• Cytological examination if atypical cells are identified
• Sexually transmitted infection screening depending on sexual history and symptoms

When Additional Care May Be Warranted

• If you have visible blood in your urine
• If you experience persistent pain during urination despite treatment
• If you develop fever, chills, or back pain along with urinary symptoms
• Recurrent urinary tract infections (more than 2 or 3 in 12 months)
• Severe pain accompanying urinary symptoms

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