A common side effect from metronidazole gel is a thick, white vaginal discharge with or without an odor which usually goes away soon after completing a full course of treatment. Metronidazole may also cause your urine to become dark which goes away when you stop using the medicine. You should not have sexual intercourse while you are being treated with metronidazole vaginal gel. Talk to your health care provider if you have any concerns about your prescribed treatment or possible side effects.