When squamous cells appear in the urine, it may simply mean that the urine sample wasn't as clean as was required, as WebMD explains. In this case, the person whose urine is being tested may be asked to provide another sample due to probable contamination of the specimen.
Squamous cells in the urine are a type of epithelial cells, which come from the tissues lining the bladder or urethra, among other structures in the body. It's normal for epithelial cells to show up in urine, though the number of them increases in the event of inflammation or infection in the urinary system. The presence of some epithelial cells in urine can be cause for concern; for example, renal tubular epithelial cells, which come from the kidneys, may indicate a kidney problem, according to Johns Hopkins Lupus Center.
In rare cases, the presence of atypical squamous cells in the urine may indicate the presence of cancer, typically urothelial carcinoma or squamous-cell carcinoma. In women, squamous-cell carcinoma may actually be a harbinger of cervical cancer rather than actually having anything to do with the urine, as the National Center for Biotechnology Information explains. These cases are extremely rare, however, amounting to approximately 0.3 percent of those cases of squamous cells found in the urine.