In women, squamous epithelium is located at the base of the bladder and urethra, in men at the end of the urethra and foreskin. In addition, they line the inside of the vagina and perineum. Finding a small amount of squamous cells in urine is normal because these cells are constantly being renewed and replaced. Large amounts are usually caused by urine being collected after it has run down nearby areas such as the vagina, perineum or foreskin; this is referred to as contamination.

Contamination can be prevented by collecting so-called "midstream" urine.

Sometimes these epithelial cells contain conspicuous dark granules; keratohyaline granules. These contain substances that contribute to the cornification of the skin layer. Their presence is normal and should not be confused with bacteria.