Squamous cells in urine are not normally a cause for alarm, as they can appear without any disease being present, according to WebMD. They may, however, contaminate the test and make it less reliable, which could mean the patient may need to give another sample.
Squamous cells line the interior of many internal organs, explains WebMD, including the bladder and urethra. It is therefore a natural process that loose squamous cells are flushed out with the urine, and is not indicative of any disease. However, they represent contamination in the test and, if the level is high, may interfere with the reading of it.
In order to get a purer sample, the University of Utah recommends that the sample be taken from the first morning urine, and that the sample is collected midstream, meaning neither the first nor the last urine. That way, the urinal tract has already have been cleaned of squamous cells as well as other contaminating material, such as bacteria from the skin.
If squamous cells in a urine sample have an atypical shape, which is an unusual finding, it may be an indication of a medical problem such as squamous cell carcinoma, a cancer type, according to Cytology Stuff. Such cells are clearly differentiated from normal squamous cells.