Antibiotics can disturb the gut and cause diarrhea. New mucus with diarrhea during or after antibiotics may need medical advice because C. diff is an important possible cause. Do not take additional or leftover antibiotics unless a clinician prescribes them for a diagnosed condition.
Why antibiotics change bowel movements
Antibiotics affect bacteria beyond the infection they are meant to treat. Mild diarrhea can occur as a side effect, but some people develop C. diff infection, which causes diarrhea and inflammation of the colon and can become serious.
Contact a clinician if
- You develop repeated watery diarrhea during or after antibiotics
- There is fever, worsening cramping, abdominal tenderness, blood, or pus
- Symptoms persist or worsen
- You recently stayed in a hospital or nursing facility
- You are older, immunocompromised, or have had C. diff before
What not to do
Do not treat visible mucus with a random antibiotic. Antibiotics do not help every cause and can increase risks, including antibiotic resistance and C. diff. Ask before using anti-diarrheal medicines when C. diff or another invasive infection may be possible.
How it is evaluated
A clinician uses your symptoms and exposure history to decide whether a stool test is appropriate. A positive test must be interpreted alongside symptoms because some people can carry C. diff without active disease.
Sources
We prioritize public-health agencies and established clinical institutions. Accessed August 19, 2026.
- C. diff: Facts for Clinicians — CDC
- Diarrhea: When to see a doctor — Mayo Clinic