Cipro acts by hindering the production of certain proteins the bacteria needs to survive. Ciprofloxacin side effects include vomiting, headache, or irritability while taking Cipro. Ciprofloxacin is widely believed by physicians to be acceptable and relatively safe. Ciprofloxacin. Cipro is an orally administered antibacterial medicine used to treat infections of the prostate gland, and some sexually transmitted diseases such as gonorrhea. The whole Ciprofloxacin treatment period. As prescribed even if you feel better, as otherwise a relapse of the infection. The risks of a drug without any potential benefit.