Cipro and Flagyl target different bacteria, which is why doctors often pair them. Learn when this combo is used, how it’s dosed, and what side effects to expect. Flagyl is used to treat bacterial infections of the vagina, stomach, skin and joints. Learn about side effects, interactions and indications. Are Flagyl and Cipro the Same Thing? Flagyl, Flagyl ER, and Flagyl Injection (metronidazole) and Cipro (ciprofloxacin) are antibiotics used to treat bacterial infections. Flagyl and Cipro are different types of antibiotics. Flagyl is a nitroimidazole antibiotic and Cipro is a quinolone antibiotic. Taking Flagyl (Metronidazole) and Cipro (Ciprofloxacin) Together Yes, Flagyl (metronidazole) and Cipro (ciprofloxacin) can be safely taken together and are actually recommended in combination for certain infections. 1, 2 Metronidazole belongs to the class of medicines known as antibiotics. It works by killing bacteria or preventing their growth. However, this medicine will not work for colds, flu, or other virus infections. This medicine is available only with your doctor's prescription. Flagyl (metronidazole) and Cipro (ciprofloxacin) are both types of antibiotics used to treat bacterial infections. Flagyl also is used to treat some parasitic infections. Ciprofloxacin (Cipro) and metronidazole (Flagyl) should be dosed at 400 mg every 8 hours and 500 mg every 6 hours, respectively, for the treatment of intra-abdominal infections in non-critically ill patients with beta-lactam allergy. Metronidazole, sold under the brand name Flagyl and Metrogyl among others, is an antibiotic and antiprotozoal medication. [10] It is used either alone or with other antibiotics to treat pelvic inflammatory disease, endocarditis, and bacterial vaginosis. [10] A moderate drug interaction exists between Cipro and Flagyl. View detailed information regarding this drug interaction. Both Cipro (ciprofloxacin) and Flagyl (metronidazole) are antibiotics, but they work in different ways to tackle infections. While these medications can be effective, they also come with potential side effects.