Can antibiotics damage organs?

Yes. One antibiotic in particular, gentamycin can harm the kidney.
Good question. Here are some examples of organ damage and their association to antibiotics- nafcillin - kidneys vancomycin- kidneys, hearing, platelets levofloxacin- tendon gentamicin- vestibular system (balance), hearing, kidneys ceftriaxone- biliary system ethambutol- eyes isoniazid- liver.
Antibiotics. Certain antibiotics can cause unexpected organ damage. A good example is in some of the more potent antibiotics that kill a significant number of normal colon flora. This leads to overgrowth of clostridial bacteria, producing an exotoxin that leads to c. Difficile colitis., with abdominal pain and diarrhea. This can become so bad that it may require total colon removal or fecal transplant.