Epithelial cells show up on nearly every urinalysis report, and in most cases they are completely normal. Your urinary tract is lined with epithelial tissue from the kidneys all the way to the opening where urine exits your body, and these cells naturally shed into urine as part of routine turnover. What matters is which type of epithelial cell appears, how many are present, and whether the sample was collected cleanly enough to trust the results. A report flagging “epithelial cells” can mean anything from a poorly collected specimen to an early sign of kidney damage, depending on context.
The Three Types and Why They Matter
Not all epithelial cells in urine carry the same meaning. Labs generally classify them into three categories based on where they originate in the urinary tract, and each tells a different story.
- Squamous epithelial cells: These are large, flat cells that line the outer urethra and, in women, the vaginal area. They are the most common type found in urine and almost always reflect skin or genital contamination rather than a problem inside the urinary tract. Finding a few is routine; finding many usually means the sample picked up cells from surrounding tissue during collection.
- Transitional (urothelial) cells: These line the bladder, ureters, and the inner part of the urethra. A small number can appear normally, but elevated counts may point to urinary tract infections, inflammation, or, less commonly, bladder tumors.
- Renal tubular epithelial cells: These originate in the tiny tubes inside the kidneys that filter and process your blood. They are not supposed to appear in significant numbers. When they do, it usually signals kidney injury or disease, and clinicians pay close attention.
A standard urinalysis report often lumps all epithelial cells together under a single line, which can be confusing. The clinical value depends entirely on which category predominates, something that sometimes requires a trained microscopist to sort out.
When Squamous Cells Signal a Bad Sample
If your urinalysis report shows a high number of squamous epithelial cells, the most likely explanation is contamination during collection. This is especially common in women, where vaginal epithelial cells easily mix into a urine sample. The presence of these cells does not mean you are sick; it means the sample may not accurately reflect what is happening inside your urinary tract.
Research has shown that squamous cell contamination genuinely undermines the usefulness of a urine test. A study analyzing over 6,400 paired urinalysis and culture results found that when squamous epithelial cells were present, the diagnostic accuracy of individual urinalysis markers dropped across the board. Tests for pyuria, bacteria, and leukocyte esterase all performed worse in contaminated samples, and contaminated specimens also had much higher rates of mixed-growth cultures that are hard to interpret.1PubMed. Squamous epithelial cell presence reduces accuracy of urinalysis for prediction of positive urine cultures The practical takeaway is that if your sample is loaded with squamous cells, your doctor may ask you to repeat it with a cleaner technique.
Interestingly, one older study found that the relationship between squamous cells and contamination is weaker than many clinicians assume. In catheterized urine samples from women, squamous cells did not predict bacterial contamination at all. Even in midstream clean-catch samples, the overall predictive value of squamous cells for contamination was only about 21%.2PubMed. Squamous cells as predictors of bacterial contamination in urine samples So while heavy squamous cell counts are a red flag for a messy specimen, a handful of squamous cells does not automatically invalidate the test. The threshold most labs use is roughly five or more squamous cells per high-power field before they label a sample as likely contaminated.
Why Clean-Catch Instructions Do Not Help as Much as You Would Think
You have probably been handed a set of instructions in a clinic telling you to wipe first and catch the urine midstream. It seems like it should reduce contamination, and the logic is sound. But the evidence that these instructions actually improve sample quality is surprisingly thin.
One emergency department study compared contamination rates before and after posting written clean-catch instructions in restrooms. Out of hundreds of samples in each group, the contamination rate for urinalysis was essentially identical: about 52% in both the instruction group and the historical control group.3The Journal of Emergency Medicine. The Effect of Written Posted Instructions on Collection of Clean-Catch Urine Specimens in the Emergency Department A separate study tried a mobile app with step-by-step visual instructions and found the same result: no significant reduction in contamination overall or when broken down by sex.4PubMed. Use of a midstream clean catch mobile application did not lower urine contamination rates in an ED
This does not mean you should skip the clean-catch technique. It likely helps some people some of the time. But it does mean that if your sample comes back flagged for epithelial contamination, it is not necessarily your fault. Emergency departments in particular deal with contamination rates around 50%, and even ideal technique cannot guarantee a pristine sample in a busy clinical setting. When a truly clean specimen is critical, clinicians may opt for a catheterized sample instead.
Transitional Cells and What Elevations Can Mean
Transitional epithelial cells, also called urothelial cells, line the bladder and the rest of the upper urinary tract. A few in your urine are normal. They shed slowly as part of the tissue’s natural cycle. But when these cells appear in large numbers or look abnormal under the microscope, clinicians start thinking about what might be irritating or damaging the bladder lining.
Common causes of elevated transitional cells include urinary tract infections, kidney stones, catheter use, and inflammation from medications. In men, a study examining first-catch urine found that the vast majority of samples contained transitional cells regardless of whether the men had urethritis or not. Around 87% of samples had transitional cells present, and there was no significant difference in cell counts between men with and without urethritis.5PubMed Central. Quantitative analysis of epithelial cells in urine from men with and without urethritis: implications for studying epithelial: pathogen interactions in vivo That said, some men with urethritis did have relatively high transitional cell counts, suggesting that inflammation can push numbers up even if it does not reliably do so across the board.
The more serious concern with abnormal transitional cells is bladder cancer. Urine cytology, where a pathologist examines shed urothelial cells under a microscope looking for cancerous changes, has been a standard screening and surveillance tool for decades. It works reasonably well for detecting high-grade tumors, which tend to shed cells that look clearly abnormal. However, its reliability for grading tumors is limited. One study found that pathologists agreed poorly on tumor grade when reading cytology slides, with inter-observer agreement falling below the threshold for even “fair” consistency in most pairings.6PubMed Central. Accuracy of grading of urothelial carcinoma on urine cytology: an analysis of interobserver and intraobserver agreement Overall accuracy was around 77%, but the variability between readers highlights why cytology alone is rarely the final word on a bladder cancer diagnosis. Cystoscopy, where a camera is passed into the bladder, remains the gold standard.
Renal Tubular Epithelial Cells and Kidney Injury
Renal tubular epithelial cells are the ones clinicians worry about most. These small, round cells come from the filtering tubes deep inside the kidney, and their presence in urine typically means those tubes are being damaged. The most common scenario is acute tubular necrosis, a form of acute kidney injury where the tubular cells die and slough off into the urine.
A systematic review found that the number of renal tubular epithelial cells and the casts they form (cylindrical structures molded by the tubule shape) are useful for diagnosing acute tubular necrosis and may even help predict whether kidney function will recover or whether dialysis will be needed.7PubMed. Acute tubular necrosis and pre-renal acute kidney injury: utility of urine microscopy in their evaluation- a systematic review In clinical practice, this distinction matters because the treatment for prerenal acute kidney injury (caused by dehydration or low blood flow) is very different from the treatment for intrinsic kidney damage.
A scoring system based on these cells and casts has proven useful in hospitalized patients. When doctors already suspected acute tubular necrosis and the urine sediment showed renal tubular cells or casts, the positive predictive value was very high. In the opposite scenario, where the clinical picture looked more like dehydration-related kidney trouble, a clean urine sediment without these cells had a sensitivity and specificity around 73–75% for confirming the prerenal diagnosis.8PubMed Central. Diagnostic value of urine microscopy for differential diagnosis of acute kidney injury in hospitalized patients In short, the presence or absence of renal tubular cells in the urine genuinely changes clinical decisions in the hospital.
Beyond acute injury, research has explored whether detecting glomerular epithelial cells, specifically podocytes, in urine could serve as a noninvasive window into kidney diseases like glomerulonephritis or diabetic nephropathy. The concept is appealing because podocytes do not normally shed in healthy kidneys, so finding them would theoretically signal active glomerular damage. However, this remains largely a research tool, with few studies having systematically tested it in clinical practice.9PubMed Central. Glomerular epithelial cells in the urine: what has to be done to make them worthwhile?
Decoy Cells After Kidney Transplant
One specialized context where epithelial cells in urine get intense scrutiny is after a kidney transplant. Transplant recipients are given immunosuppressive drugs to prevent rejection, and that suppressed immune system can allow viruses to reactivate. BK polyomavirus is one of the most common culprits, and it infects the epithelial cells lining the transplanted kidney and urinary tract.
When BK virus takes hold, it transforms infected epithelial cells into what pathologists call “decoy cells.” These have enlarged nuclei with a glassy appearance and a distinctive inclusion pattern that mimics cancer cells under the microscope, hence the name “decoy.” One study found decoy cells in about 15% of kidney transplant recipients screened.10PubMed Central. Bright Field Microscopy to Detect Decoy Cells Due to BK Virus Infection in the Fresh and Unstained Urine Sediment in Kidney Allograft Recipients Their presence is one of the earliest markers that the virus is reactivating, and monitoring trends in decoy cell counts can help predict whether a patient will develop BK viremia, the stage where the virus enters the bloodstream and threatens the transplant.
Counting decoy cells over time appears to be more informative than a single snapshot. Research comparing transplant recipients who developed BK viremia with those who did not found that the maximum decoy cell count was significantly higher in the viremia group. The viremia group also showed an increasing trend in decoy cell numbers over time, while the non-viremia group showed a decreasing trend. There was a strong positive correlation between decoy cell counts and the amount of BK virus DNA measured by molecular testing.11PubMed Central. Prediction of Early BK Virus Infection in Kidney Transplant Recipients by the Number of Cells With Intranuclear Inclusion Bodies (Decoy Cells) For transplant teams, tracking these cells in urine cytology is a relatively simple way to catch a dangerous infection before it damages the graft.
Pregnancy and Misleading Results
Pregnant women frequently get urinalysis tests, and their results are unusually prone to confusion around epithelial cells. Hormonal changes during pregnancy increase vaginal discharge and the shedding of epithelial cells from the genital tract, which means clean-catch samples are harder to collect cleanly. But there is another, less obvious problem: automated urine analyzers can mistake epithelial cells for white blood cells.
A study of urine samples from pregnant women using the Sysmex UF-1000i flow cytometer found a strikingly high false positive rate for white blood cells. The machine flagged about 73% of samples as positive for white blood cells, while manual microscopy confirmed only about 19% were truly positive. Meanwhile, the machine underreported epithelial cells, detecting them in about 37% of samples versus 73% by microscopy. The correlation analysis showed that the false white blood cell readings were driven by epithelial cells being misclassified by the instrument.12PubMed Central. High false positive rate of white blood cells in urine samples of pregnant women may be caused by epithelial cells being misclassified by the sysmex UF-1000i urine flow cytometer
This matters because elevated white blood cells in urine are a primary sign of urinary tract infection. If the analyzer is flagging epithelial cells as white cells, a pregnant woman could be diagnosed with a UTI she does not have, leading to unnecessary antibiotics. Clinicians who work with pregnant patients learn to double-check automated results with manual microscopy when the numbers look suspicious.
Newborns and Baseline Shedding
Parents of newborns may encounter epithelial cells on an early urinalysis and wonder whether something is wrong. In healthy newborns, epithelial cell shedding is quite common, especially in the very first urine samples after birth. One study of healthy neonates found that about 29% of first-void samples had more than five epithelial cells per high-power field, a level that would be considered mildly elevated in an adult. By the second urine sample, this dropped to about 18%.13Clinical and Experimental Pediatrics. Urine Sediments and Protein in Healthy Newborn Infants The likely explanation is that the newborn urinary tract is adjusting to functioning independently, and the initial shedding settles down quickly. Unless there are other abnormal findings in the urine, epithelial cells alone in a newborn sample are generally not a cause for alarm.
How Labs Count Epithelial Cells
Traditionally, epithelial cells are counted by a trained technician looking at urine sediment under a microscope, typically reported as cells per high-power field. This is the gold standard but slow, subjective, and labor-intensive. Modern labs increasingly rely on automated urine analyzers that use flow cytometry or digital imaging to classify and count particles in urine.
These machines have improved considerably. A comparison of the newer Sysmex UF-5000 analyzer against its predecessor, the UF-1000i, showed a substantial jump in accuracy for detecting epithelial cells. Sensitivity rose from about 43% on the older model to about 77% on the newer one, and the positive predictive value climbed from roughly 33% to nearly 80%. Agreement with manual microscopy also improved dramatically.14Annals of Clinical & Laboratory Science. Sysmex UF-5000 Automatic Urine Sediment Analyzer Can Improve the Accuracy of Epithelial Cell Detection A separate evaluation found good agreement between two different automated platforms and manual microscopy for epithelial cells, red blood cells, and white blood cells across 250 samples.15PubMed. Performance of automated urine analyzers using flow cytometric and digital image-based technology in routine urinalysis
Still, automation is not perfect. As the pregnancy data showed, certain patient populations produce urine samples that confuse these instruments. Epithelial cells that are unusually large or clumped can be miscounted, and the machines cannot distinguish between squamous, transitional, and renal tubular cells with the same confidence a skilled microscopist can. When the clinical stakes are high, manual review of the sediment remains essential.
Urine-Derived Stem Cells
One area of research that has nothing to do with disease diagnosis but everything to do with epithelial cells in urine is regenerative medicine. Scientists have discovered that among the epithelial cells shed into urine, a small population behaves like stem cells. These urine-derived stem cells can be collected noninvasively and reprogrammed into induced pluripotent stem cells, which can theoretically become any cell type in the body.
What makes urine-derived cells attractive for this purpose is efficiency. They reprogram faster and at higher rates than cells taken from other tissues. One analysis reported that urine-derived cells achieve around an 80% transduction rate compared to about 50% for other common cell sources, and they show signs of reprogramming within three days rather than the weeks required for other cell types.16Journal of Biomedical Science. Exploiting urine-derived induced pluripotent stem cells for advancing precision medicine in cell therapy, disease modeling, and drug testing The practical appeal is obvious: collecting cells from urine is painless and can be done repeatedly, unlike tissue biopsies. Research groups are exploring these cells for personalized disease modeling, drug testing, and eventually cell-based therapies, turning what most of us flush away into a potential medical resource.