Squamous epithelial cells in urine are flat, thin cells that line the outer portions of the urinary tract, the vagina, and the outer skin of the genital area. When they show up on a urinalysis report, it usually means the urine sample picked up skin cells during collection rather than signaling a problem inside the urinary tract. A normal result is “few” cells, and anything labeled “moderate” or “many” typically points to a contaminated sample that may need to be recollected.
Where These Cells Come From
Squamous epithelial cells are the body’s surface-level lining cells. They cover the skin, mouth, throat, esophagus, and the outer portions of the genitourinary tract. In the context of a urine test, they most commonly originate from the skin around the urethra, the vaginal lining, or the foreskin. They are not cells from the kidneys or the bladder itself.
Because they sit on the outermost surfaces, these cells naturally shed in small numbers all the time. When urine passes over that skin on its way into a collection cup, it can sweep some of those cells along. That’s why their presence on a lab report is generally treated as a collection issue, not a medical finding.
What Your Lab Results Mean
Most labs report squamous epithelial cells in broad categories: “few,” “moderate,” or “many” rather than precise counts. A result of “few” is considered normal and doesn’t require any follow-up. A result of “moderate” or “many” raises a flag that the sample likely contains material from the skin rather than purely from the urinary tract.
This matters because contamination can throw off other parts of the urinalysis. If a lab is checking for bacteria to diagnose a urinary tract infection, for instance, skin bacteria that washed into the cup alongside those epithelial cells can produce a misleading result. The 2025 American Urological Association guidelines note that when a significant number of squamous cells are present, contamination is possible and a repeat specimen collection should be considered.
Three Types of Epithelial Cells in Urine
Not all epithelial cells on a urine report carry the same meaning. Labs distinguish between three types, and knowing the difference helps you read your results more accurately.
- Squamous epithelial cells come from the outer genital skin and the lower urethra. They are the largest of the three types and almost always indicate contamination from the skin surface during collection. On their own, they are not a sign of disease.
- Transitional epithelial cells line the bladder, ureters, and the upper urethra. A small number can be normal, but elevated counts may suggest inflammation or irritation of the bladder lining.
- Renal tubular epithelial cells come from the kidney’s filtering tubes. Even a small number of these is considered abnormal and can point to kidney damage or disease. These are the cells that prompt the most concern from a healthcare provider.
If your report specifically says “squamous,” that’s the least worrisome of the three. It’s worth noting which type was identified, because the clinical significance is very different for each.
Why Contamination Happens
The most common reason for high squamous cell counts is simply that the genital area wasn’t cleaned thoroughly enough before collecting the sample. Urine tests typically use what’s called a “clean catch” method, which is designed to minimize skin contact. If any step is skipped or rushed, shed skin cells end up in the cup.
Women tend to have higher squamous cell counts on urine tests than men because the urethra is shorter and sits closer to the vaginal opening, where squamous cells are abundant. This makes proper collection technique especially important.
How to Collect a Clean Sample
If your provider asks you to repeat a urine test because of contamination, the goal is a “clean catch midstream” sample. Ideally, collect the sample when urine has been sitting in your bladder for two to three hours so you have enough volume to work with.
For People With a Vagina
Wash your hands with soap and warm water. Sit on the toilet with your legs apart and use two fingers to spread the labia open. Using a sterile wipe, clean the inner folds of the labia from front to back. Use a second wipe to clean over the urethral opening, just above the vaginal opening. Keep the labia spread apart, urinate a small amount into the toilet to flush away cells sitting near the opening, then hold the collection cup a few inches from the urethra and fill it about halfway. Finish urinating into the toilet.
For People With a Penis
Wash your hands, then clean the head of the penis with a sterile wipe. If uncircumcised, retract the foreskin first. Urinate a small amount into the toilet, then collect the midstream portion into the cup until it’s about half full. Finish into the toilet.
In both cases, screw the lid on tightly without touching the inside of the cup or lid. The key principle is the same: the first bit of urine flushes away surface cells, and the midstream portion is the cleanest representation of what’s actually in the bladder.
When Squamous Cells Might Signal Something More
In rare cases, persistently elevated squamous epithelial cells, even with proper collection technique, can reflect chronic irritation or inflammation of the lower urinary tract or genital tissues. Vaginal infections, for instance, can increase the rate at which squamous cells shed. Chronic skin conditions affecting the genital area can do the same.
The cells themselves aren’t harmful. What matters is the context: if your provider ordered the urinalysis to check for infection or kidney problems, a contaminated sample means those results can’t be trusted, and the test needs to be repeated. If the retest comes back clean with only a “few” squamous cells, the original finding was almost certainly a collection artifact and nothing to worry about.