Flagyl (Metronidazole) Dosage and Side Effects FLAGYL works by killing bacteria and parasites that cause infections in your body. It can be used to treat: infections of the genital tract (such as trichomoniasis: a sexually transmitted infection, bacterial vaginosis); stomach, liver and intestinal infections (amebiasis, giardiasis); infections (such as intra-abdominal, brain … Continue reading Flagyl (Metronidazole)