Clue cells are certain cells in the vagina that appear fuzzy without sharp edges under a microscope. They are epithelial cells that get their distinctive stippled appearance by being covered with bacteria, particularly Gardnerella vaginalis, a group of Gram-variable bacteria. Clue cells are a medical sign of bacterial vaginosis, which is characterized by a foul, fishy smelling, thin gray vaginal discharge, and an increase in vaginal pH from around 4.5 to over 5.5.

Clue cells are not associated with urinary tract infections or positive urine cultures. They are an accepted clue to the diagnosis of bacterial vaginosis, but there is no consensus about what should be regarded as a clue cell. Each investigator has their own highly subjective and even individually not reproducible feeling of what a clue cell already is and what it is still not.