The Risks and Side Effects of UTI Antibiotics

Antibiotics are medications used to treat infections caused by bacteria. E. coli is the most common cause of bacterial urinary tract infections (UTIs). A UTI involves any part of your urinary tract—the bladder, kidneys, ureters, and urethra. If your healthcare provider suspects you have a bacterial UTI, they may choose to start you on an antibiotic. To help your doctor determine the best antibiotic based on your urine culture results, it is essential to share the following details:

  • If you are pregnant or breastfeeding
  • Are over 65 years old
  • Have a history of UTIs or side effects from antibiotics
  • Have any allergies to medicines, including antibiotics

Antibiotics are necessary for treating bacterial infections but can cause side effects. This article will provide information on common and potential side effects, the likelihood of experiencing them, and the side effects associated with long-term antibiotic use.

Potential Side Effects of Taking Antibiotics to Treat a UTI

Some of the side effects specific to antibiotics for UTIs are harmless. Notify your provider immediately if you experience any of the more serious side effects described below.


Nitrofurantoin (Macrobid) is the most commonly prescribed antibiotic for UTIs. You may notice your urine turning dark yellow or brown while taking nitrofurantoin. This side effect is harmless and will stop once you finish the medication.

More severe side effects include 

  • Lung problems (e.g., a cough that doesn't stop, chest pain, difficulty breathing),
  • A severe headache or headache that doesn't go away,
  • New signs of infection (fever),
  • Bruising or bleeding easily,
  • Changes in mental status or mood, 
  • And vision changes. 

Other rare but severe side effects include liver disease and blood or nerve problems. Signs of these problems can be persistent nausea/vomiting, increased tiredness, dark urine, yellowing of the eyes and skin, a fast heartbeat, unusual sensations (numbness/tingling) in the arms and legs, and muscle weakness.

Ciprofloxacin and Levofloxacin

Healthcare professionals use Ciprofloxacin (Cipro) and Levofloxacin (Levaquin), or fluoroquinolones, to treat many bacterial infections. They work by stopping bacteria from multiplying. More severe side effects include easy bleeding or bruising and signs of a new infection (fever or sore throat that does not go away). Other potential side effects unique to fluoroquinolones include peripheral neuropathy and tendinopathy

Serious but rare side effects of these antibiotics include liver and kidney problems. Signs of liver problems include persistent nausea/vomiting, increased tiredness, stomach pain, dark urine, and yellowing of the eyes and skin.

Seek immediate emergency assistance if you have severe dizziness, fainting, and a fast or irregular heartbeat. Another emergent—but very rare—side effect is a tear in the aorta (main blood vessel). Signs of an aortic tear include sudden severe stomach, chest, or back pain and/or shortness of breath.


Fosfomycin (Monurol) is a broad-spectrum antibiotic that can work against a wide range of bacteria. Side effects include vision change, unusual weakness, and clay-colored stools. Serious but rare side effects are similar to UTI symptoms, such as blood in the urine, burning or pain with urination, fever or chills, and low back or side pain. 


Cephalexin (Keflex) is a cephalosporin antibiotic used to treat bacterial infections, including ear and skin infections. Cephalexin can cause fungal infections if used for long periods. Signs of fungal infections include white patches in your mouth or a vaginal yeast infection. A severe but rare side effect involves the skin, causing redness, blistering, peeling, and loosening. The blistering and peeling may start as a red or purple rash and can occur weeks to months after finishing the antibiotic. 


Trimethoprim-Sulfamethoxazole (Bactrim) is a combination of two antibiotics. Healthcare providers use it to treat many different bacterial infections. Serious side effects of this antibiotic include muscle weakness, mental or mood changes, kidney problems, extreme drowsiness, and low blood sugar. Signs of low blood sugar are sweating, shaking, a fast heart rate, hunger, blurred vision, dizziness, and tingling in the hands and feet.

Seek emergency help if you have a headache that doesn't go away, neck stiffness, seizures, or a slow/irregular heartbeat.

Allergic Reactions and Anaphylaxis

Allergic reactions and anaphylaxis are not common but can be severe. Symptoms of anaphylaxis include

  • Shortness of breath,
  • Severe vomiting,
  • Lightheadedness and severe dizziness,
  • Fast heart rate,
  • Hives (a rash that looks like mosquito bites but the rash moves around),
  • And swelling of the face, lips, or tongue.

You should seek emergency help (call 9-1-1) for signs of anaphylaxis. 

Clostridium difficile

Clostridium difficile (C. diff) infection is a side effect of antibiotic use. It is a bacterial infection that can start while on antibiotics or shortly after. Anyone can develop C. diff, but certain risk factors include being 65 years or older, having had a previous infection with C. diff, and having a weakened immune system. Symptoms of C. diff include

  • Watery diarrhea (can be up to 10 to 15 times daily), 
  • Severe abdominal cramping and pain, 
  • Fever, 
  • And nausea. 

How Likely Is It That I Will Experience Side Effects from Antibiotics for a UTI?

All medications have the potential for side effects, including antibiotics. Your provider decided to treat you with antibiotics because the benefit of treatment is greater than the risk of experiencing side effects. Some people may experience side effects, but less than 1% experience more severe side effects.  

About 10-20% of patients experience common side effects. The common side effects you may encounter should resolve after finishing your prescription. Many common side effects are similar to symptoms of a UTI (abdominal pain, nausea, and vomiting). Even though they are standard and relatively non-bothersome, there may be simple solutions to help decrease these side effects. Contact your provider to share what you are experiencing and discuss solutions.

Common Side Effects Associated with Antibiotics for a UTI

Antibiotics destroy the bacteria (bactericidal) or stop it from growing (bacteriostatic). Even though the intended target is the infection-causing bacteria, the antibiotics will kill the good bacteria in the digestive system (normal gut flora). Disrupting normal body flora is the primary cause of common side effects.

Gastrointestinal symptoms are the most common side effects of antibiotic use. These symptoms include

  • Abdominal pain,
  • Nausea and vomiting,
  • Diarrhea,
  • And fungal infections.

Antibiotics can also irritate the stomach wall lining, which can cause abdominal pain. 

Normal body flora prevents fungus from growing on the skin and mucosa. Mucosa is a special covering in part of the respiratory system (i.e., nose), gastrointestinal system, and reproductive system (i.e., vagina). 

Fungal infections are more likely to occur when antibiotics destroy the normal body flora. You should contact your doctor if you have symptoms of a fungal infection. Signs of fungal (Candidal) infection include white patches on the skin or inside of the mouth and itching, pain, redness, and thick, white discharge from the genital area.

Damage to normal body flora from UTI antibiotics can also cause the side effect of fatigue, resulting from impaired nutrient absorption. Other medications, including antidepressants and antihistamines, can worsen fatigue or drowsiness when taken with UTI antibiotics.

In addition, UTI antibiotics can cause dizziness and headaches. Headaches associated with UTI antibiotics are more common in older patients and those with underlying medical conditions.

Can Long-term Use of Antibiotics for a UTI Cause Any Permanent Side Effects?

Antibiotic resistance is the most concerning permanent side effect of the long-term use of antibiotics. It occurs when bacteria change and can defeat the antibiotics that once killed them. When antibiotics are used for longer periods or more often, they may become less effective against the bacteria they once treated. Some bacteria are now superbugs and are multidrug-resistant (MDR). This can also mean that illnesses that were once treated at home may require hospital admission for intravenous antibiotics.  

It is crucial for patients and their providers to discuss the need for antibiotics to treat an illness and for patients to complete the entire course of antibiotics, even if they are feeling better. 

Many healthcare systems are emphasizing antimicrobial stewardship. Antimicrobials are medicines used to kill microbes (bacteria and fungi). These programs help healthcare providers safely and appropriately prescribe antibiotics to decrease the number of side effects and drug-resistant organisms.


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Laura Kim

Author Bio: Laura M. Kim, DNP, PNP-PC/-AC, RN 

Laura Kim is a pediatric nurse practitioner and registered nurse. She has been caring for pediatric patients since 2009. She strives to make patient education accessible to all patients. Collaborated with Global Health Media and local translator to develop breastfeeding education videos for Chuukese families. Served as adjunct faculty at the University of Guam School of Nursing in the Department of Women and Children’s Health from 2018 to 2019.