Pregnancy-Safe Antibiotics: What You Need to Know About Side Effects and Counseling

What Makes an Antibiotic Safe During Pregnancy?

Not all antibiotics are created equal when you’re pregnant. Some can cross the placenta and affect your baby’s development, while others have been studied for decades and shown to be safe. The goal isn’t to avoid antibiotics altogether-it’s to pick the right one for the right infection. About 15 to 20% of pregnant people will need an antibiotic at some point during their pregnancy, most often for a urinary tract infection. Left untreated, these infections can lead to preterm labor, kidney infections, or even sepsis. So the real risk isn’t the medicine-it’s the infection if you don’t treat it.

The safest antibiotics fall into two main groups: penicillins and cephalosporins. These are beta-lactam drugs, meaning they attack bacteria without harming human cells. Amoxicillin, for example, is used in more than half of all antibiotic prescriptions during pregnancy. It reaches the baby in about half the concentration of the mother’s blood, but studies tracking over 130,000 pregnancies show no increase in birth defects. Cephalexin works the same way and is often used if someone has a mild penicillin allergy. Both are considered Category B, meaning animal studies showed no risk and human data supports safety.

Common Side Effects You Might Experience

Even the safest antibiotics can cause side effects-and knowing what to expect helps you stay on track with your treatment. The most common issue is stomach upset. About 15 to 20% of people taking amoxicillin feel nauseous, especially on an empty stomach. Diarrhea is even more common, affecting up to 25% of users, depending on the drug. This isn’t always harmless. If diarrhea lasts more than 48 hours after finishing the course, or if you have blood in your stool or severe cramping, it could be a sign of Clostridioides difficile infection, a serious gut problem that can develop after antibiotics kill off good bacteria.

Another frequent complaint is yeast infections. Antibiotics don’t just target bad bacteria-they also reduce the good ones that keep yeast in check. Vaginal itching or thick, white discharge isn’t rare during pregnancy anyway, but antibiotics can make it worse. Over-the-counter antifungal creams are safe to use during pregnancy and often help. Don’t delay treatment just because you think it’s "normal." Left untreated, yeast infections can increase the risk of preterm rupture of membranes.

Some antibiotics, like clindamycin, are linked to a higher chance of diarrhea and C. diff. That’s why doctors often avoid it unless it’s needed-for example, if you’re allergic to penicillin or have bacterial vaginosis that didn’t respond to other treatments. Metronidazole, while safe in the second and third trimesters, can cause a metallic taste in your mouth. It’s unpleasant but harmless. If nausea is bad, take your pills with food. For amoxicillin, that’s actually recommended. For others, like nitrofurantoin, taking it with meals reduces stomach upset and helps your body absorb it better.

Antibiotics to Avoid During Pregnancy

There are clear red flags. Tetracyclines-including doxycycline and minocycline-are absolutely off-limits after the fifth week of pregnancy. These drugs bind to developing bones and teeth, causing permanent tooth discoloration in your baby. The teeth can turn yellow, gray, or brown. They also interfere with bone growth. Even a short course can cause lasting damage.

Sulfonamides like Bactrim (trimethoprim-sulfamethoxazole) are tricky. They’re fine later in pregnancy, but if taken in the first trimester, they’re linked to a 2.6 times higher risk of neural tube defects like spina bifida. That’s why many doctors avoid them entirely unless no other option exists. Aminoglycosides like gentamicin are used only in serious infections like sepsis because they can damage the baby’s hearing. Even at therapeutic doses, up to 20% of exposed babies may develop sensorineural hearing loss. These drugs require careful blood level monitoring and are rarely used unless you’re in the hospital.

Macrolides like erythromycin and clarithromycin carry a small but real risk: infantile hypertrophic pyloric stenosis. This is a condition where the muscle at the bottom of the stomach thickens, blocking food from entering the intestine. It’s rare-about 1 in 500 babies-but the risk jumps 2.3 times if the mother took these antibiotics in the first trimester. Azithromycin, however, doesn’t carry the same risk and is now preferred for chlamydia and other infections.

Fluoroquinolones like ciprofloxacin and levofloxacin are banned in Europe during pregnancy. In the U.S., they’re technically not approved but may be used in life-threatening cases where no other drug works. Animal studies show joint damage in developing fetuses, and while human data from the Danish National Birth Cohort found no increased risk of musculoskeletal problems, most doctors still avoid them unless there’s no alternative.

How Your Doctor Picks the Right Antibiotic

Your doctor doesn’t just pick a random antibiotic. They think about three things: what infection you have, how far along you are, and what your allergies are. For a simple bladder infection, nitrofurantoin is often the first choice after the first trimester. It doesn’t cross the placenta much, so the baby gets very little of it. For a kidney infection, ceftriaxone or ampicillin are given by IV in the hospital. For Group B Strep, which every pregnant person is screened for at 36 weeks, penicillin or cefazolin are standard during labor to prevent newborn sepsis.

If you think you’re allergic to penicillin, don’t assume it’s true. Studies show 90% of people who say they’re allergic to penicillin can actually take it safely. Many people had a rash as a kid and were labeled allergic, but that wasn’t a true allergy. A simple skin test or oral challenge can confirm whether you’re truly allergic. If you are, clindamycin or vancomycin are alternatives-but those come with their own risks, like higher chances of C. diff. So getting your allergy properly checked matters.

Doctors also avoid broad-spectrum antibiotics unless necessary. Amoxicillin-clavulanate (Augmentin) might seem like a stronger option, but it’s linked to an 1.8 times higher risk of maternal diarrhea than plain amoxicillin. That’s why most guidelines recommend sticking with plain amoxicillin unless the infection is resistant.

What Good Counseling Looks Like

Most people don’t know what to ask when they’re handed an antibiotic prescription during pregnancy. Good counseling answers four key questions: Why are you giving me this? Is it really safe? What side effects should I watch for? And what happens if I don’t finish the course?

For example, if you’re prescribed amoxicillin for a UTI, your provider should explain that untreated UTIs can lead to preterm labor. They should mention that amoxicillin has been studied in over 100,000 pregnancies with no increase in birth defects. They should warn you about nausea or diarrhea and tell you to take it with food. And they should stress that even if you feel better after two days, you still need to finish all seven or ten pills. Stopping early can let resistant bacteria survive-and next time, the same drug might not work.

Research shows that when patients get this kind of clear, specific counseling, they’re 37% less likely to stop the antibiotic early. They’re also 29% more likely to take it correctly. That’s not just about compliance-it’s about preventing antibiotic resistance, which is growing fast. The CDC estimates that 30 to 40% of antibiotic prescriptions in outpatient settings are unnecessary or inappropriate. Many are given for viral infections like colds or flu, which antibiotics can’t touch. That’s why it’s important to ask: "Is this infection bacterial?" If it’s not, you don’t need an antibiotic at all.

What’s New in 2025?

Things are changing. For years, pregnant people were left out of clinical trials. That meant we didn’t have good data on how drugs behaved in pregnancy. Now, the FDA is pushing drug companies to include pregnant women in studies. In January 2024, the NIH launched the Antimicrobial Resistance in Pregnancy (AMRIP) study, tracking 15,000 pregnancies to see how antibiotics affect newborns-especially those exposed in the third trimester.

There’s also new data on azithromycin. Earlier concerns about heart defects have been ruled out. A 2024 update from ACOG says the risk is no higher than in unexposed pregnancies. That means azithromycin is now a stronger option for chlamydia and other STIs during pregnancy.

But gaps remain. Over 60% of antibiotics used in pregnancy still lack solid human safety data. Newer drugs like tedizolid or delafloxacin are being used more often, but we don’t know their long-term effects on babies. That’s why sticking with well-studied drugs like amoxicillin and cephalexin remains the best practice.

What You Can Do

• Always tell your provider if you’ve ever had a reaction to any antibiotic-even if it was years ago.
• Ask: "Is this infection bacterial?" If not, you don’t need antibiotics.
• Take your antibiotic exactly as directed. Don’t skip doses or stop early.
• Report persistent diarrhea, rash, or unusual symptoms right away.
• If you’re prescribed a new antibiotic, ask if it’s been studied in pregnancy and what the data says.
• Keep a list of all medications you take during pregnancy, including over-the-counter and supplements.

Antibiotics during pregnancy aren’t something to fear-they’re a tool. Used correctly, they protect you and your baby. Used carelessly, they can cause harm. The key is knowing which ones are safe, what side effects to expect, and how to use them properly. You’re not alone in this. Millions of pregnant people have taken these medications safely. With the right information, you can too.