Metronidazole (often known as Flagyl) is a frequently prescribed medication used to treat a wide variety of bacterial and parasitic infections. It is a powerful antimicrobial agent effective against certain anaerobic bacteria and protozoa, including those that cause skin, dental, and reproductive tract infections. Given its systemic action, many people taking the drug experience changes in their digestive health. This article addresses whether metronidazole affects bowel movements, detailing the mechanisms and potential complications within the gastrointestinal system.
Common Gastrointestinal Effects
Metronidazole is highly likely to cause changes in bowel habits, with loose stools or mild diarrhea being among the most commonly reported side effects. This temporary change is a frequent and expected response to the medication. These digestive disturbances are typically transient, often resolving on their own once the full course of treatment is completed.
Patients frequently report other non-severe gastrointestinal symptoms alongside changes in stool consistency. Nausea and vomiting are common, and taking the medication with food can help mitigate these effects. Many people also notice a distinct metallic taste in their mouth, a signature side effect that usually disappears soon after the final dose. Mild abdominal cramping and general upset stomach are also typical signs of adjustment.
How Metronidazole Disrupts Gut Function
The digestive changes occur because metronidazole is a broad-spectrum antimicrobial that cannot differentiate between harmful pathogens and beneficial gut bacteria. The drug works by disrupting the DNA of susceptible microorganisms, leading to cell death of the target infection. A significant portion of the healthy bacterial population residing in the intestines is also inadvertently affected.
This widespread reduction in microbial diversity causes dysbiosis, an imbalance in the gut microbiota. Beneficial bacteria, such as those that aid in digestion and stool formation, are temporarily depleted, directly impacting normal gut function. The resulting imbalance can increase intestinal motility and alter fluid absorption, leading to loose stools and diarrhea.
Recognizing Signs of Serious Complications
While mild diarrhea is common, it is important to distinguish it from a more severe complication that can occur with nearly any broad-spectrum antibiotic. The disruption of the gut flora can sometimes allow for the opportunistic overgrowth of a toxin-producing bacterium called Clostridioides difficile. This causes an infection known as C. diff colitis, a serious risk that requires immediate medical attention and is distinct from routine antibiotic-associated diarrhea.
Specific red flag symptoms indicate a potential C. diff infection or other severe adverse reaction. These signs include diarrhea that is frequent, watery, and persistent, especially if it continues for several days after the metronidazole course has finished. Severe abdominal pain, high fever, or the presence of blood or pus in the stool are urgent indicators. Experiencing these symptoms warrants immediate contact with a healthcare provider for proper testing and treatment, as severe cases can lead to serious intestinal inflammation.

