According to the website of the John Hopkins Lupus Center, squamous cells are most often contamination; the University of Utah website concurs and points specifically to contamination from the skin and the outer urethra. Contamination can enter medical samples by not washing hands or genitals and not collecting urine mid-stream, states Informed Health Online.
Squamous cells are flat, scale-like cells that cover many areas of the human body, including the skin, according to About.com. The website Cytology Stuff states that they can be found on the mucus membranes of the genitalia and the trigone of the bladder. In most cases, squamous cells found in urine samples are simply a result of contamination from the genitals due to not catching urine mid-stream. Pressing the sample cup against one's genitals, for example, can pass cells from the outside of the body into the urine being collected.
Occasionally, squamous cells are shed from the inner lining of the bladder and are thus unavoidable.
Squamous cells can also show up in urine samples due to illness. In patients with squamous carcinoma, urine samples may contain atypical squamous cells. Tumors in the urogenital region shed these cancerous cells into the urine stream. These abnormal cells may lack nuclei or have atypical shapes.