The most common use for cotton swabs is to clean the ear canal by removing earwax.

Medical-type swabs are often used to take microbiological cultures. Pharmaceutical grade cotton swabs are necessary for medical applications.^[4] These medical grade swabs are rubbed onto or into the infected area, then wiped across the culture medium, such as an agar plate, where bacteria from the swab may grow.  .

A related area is the use of swabs for microbiological environmental monitoring.\Special brands of cotton swabs exist for this purpose, characterised by sturdier cotton heads and varied shapes of those heads.

• This use is problematic, as manufacturers differ in the binders they use to fix the cotton to the stem, affecting the outcome of the test.^[6]