Basic Information. Metronidazole is an antibiotic that is used commonly to treat protozoal infections and anaerobic bacterial infections. It also has anti-inflammatory effects in the bowel. While metronidazole is meant to remedy a dog's gastrointestinal system, it can also cause adverse side effects, including vomiting, nausea, and loss of appetite. Metronidazole, marketed under the brand name Flagyl among others, is an antibiotic and antiprotozoal medication. It is used either alone or with other antibiotics to treat pelvic inflammatory disease, endocarditis, and bacterial vaginosis. It is effective for dracunculiasis, giardiasis, trichomoniasis, and amebiasis. It is an option for a first. What other drugs will affect metronidazole? Sometimes it is not safe to use certain medications at the same time. Some drugs can affect your blood levels of other drugs you take, which may increase side effects or make the medications less effective. Side effects of Prednisone in dogs! Prednisone for cough. Visit our online store. A Canadian Pharmacy offering discounts on cheap prescriptions medications. 24/7 Online support. Official Online Drugstore. There is a NEW drug on the market to control itching in dags from allergies, called Apoquel. It has been launched with much fanfare.from Zoetis. But be cautious, as its one small study showed serious side effects as it suppressed the immune system. Learn about the potential side effects of metronidazole. Includes common and rare side effects information for consumers and healthcare professionals.