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

When you're pregnant and get sick, the last thing you want is to choose between treating an infection and protecting your baby. That’s why knowing which antibiotics are safe - and what side effects to watch for - isn’t just helpful, it’s essential. About 1 in 5 pregnant people will take an antibiotic during pregnancy, mostly for urinary tract infections, dental issues, or Group B Strep. But not all antibiotics are created equal. Some are well-studied and safe. Others carry real risks. And many people are confused about what’s okay and what’s not.

Which Antibiotics Are Actually Safe During Pregnancy?

The safest antibiotics during pregnancy belong to two main families: penicillins and cephalosporins. These are the go-to choices for doctors because they’ve been used for decades in pregnant patients with no clear link to birth defects.

Amoxicillin is the most common. It’s used for everything from sinus infections to strep throat. Studies show it crosses the placenta but doesn’t harm the baby. Fetal levels reach about half of what’s in mom’s blood - and that’s fine. The American College of Obstetricians and Gynecologists (ACOG) recommends it as first-line for Group B Strep during labor. It’s also the top pick for urinary tract infections in pregnancy.

Cephalexin (brand name Keflex) is the usual alternative if someone’s allergic to penicillin. It’s just as safe, with decades of data backing it up. It’s often used for skin infections or respiratory bugs. But watch out for ceftriaxone - while effective, it can interfere with bilirubin in newborns if given right before or after delivery. That’s why it’s avoided in the final 72 hours of pregnancy unless absolutely necessary.

Clindamycin (Cleocin) is another solid option. It’s commonly used for bacterial vaginosis or dental infections. Studies show it reaches the fetus at about 30-40% of maternal levels, with no consistent signs of harm. It’s especially useful for people with true penicillin allergies.

Antibiotics with Nuanced Safety - Know the Limits

Some antibiotics are safe - but only under certain conditions. Timing matters.

Metronidazole (Flagyl) is tricky. It’s Category B, meaning animal studies showed risk, but human data hasn’t confirmed it. Still, doctors avoid oral metronidazole in the first trimester because of old rodent studies where doses were 50-100 times higher than what humans take. But if you have bacterial vaginosis in your second or third trimester? It’s often the best choice. Topical gels or creams? Even safer - they barely enter the bloodstream.

Nitrofurantoin (Macrobid) is the standard for UTIs in pregnancy - but not in the first trimester. A 2011 study of over 1,800 pregnancies found a small increase in cleft lip risk when taken early. That’s why it’s avoided in the first 12 weeks. After that? It’s one of the safest options. It doesn’t cross the placenta much, so it doesn’t reach the baby in significant amounts.

Azithromycin (Zithromax) is now considered safe for most pregnancy uses, including chlamydia. A 2020 study of nearly 46,000 pregnancies found no increased risk of birth defects. But erythromycin and clarithromycin? They’re different. A 2014 study linked them to a 2.3-fold higher risk of infantile pyloric stenosis - a condition that causes severe vomiting in newborns. So if you’re in the first trimester, stick with azithromycin if you need a macrolide.

Antibiotics to Avoid During Pregnancy

Some antibiotics have clear, well-documented risks. These are almost never used unless there’s no other option - and even then, only in emergencies.

Tetracyclines - including doxycycline - are a hard no after week 5 of pregnancy. They bind to developing bones and teeth, causing permanent gray or brown staining. The discoloration isn’t just cosmetic - it’s structural. These drugs can also slow bone growth. That’s why they’re banned in pregnancy after the first few weeks.

Sulfonamides (like Bactrim or Septra) carry a higher risk of neural tube defects if taken in the first trimester. One study showed a 2.6-fold increase. They’re also linked to jaundice in newborns because they displace bilirubin. So they’re avoided early on. Later in pregnancy? Sometimes used if no alternatives exist - but only after careful discussion.

Aminoglycosides - like gentamicin - are Category D. That means there’s evidence of harm. They can cause permanent hearing loss in the baby. If you absolutely need one - say, for a severe kidney infection - your doctor will monitor your blood levels closely. Peak levels must stay under 8-10 mcg/mL, and troughs below 1 mcg/mL. Even then, the risk of hearing damage is 10-20%.

Common Side Effects - And How to Handle Them

Even safe antibiotics can cause discomfort. Most side effects are mild, but knowing what to expect helps you stick with the full course.

• Nausea and vomiting - Happens in 15-20% of people taking amoxicillin. Take it with food. Avoid empty stomachs.
• Diarrhea - Affects 5-25% of users. Mild cases are normal. But if it lasts more than 48 hours after finishing the antibiotic, or includes blood or fever, call your provider. It could be Clostridioides difficile (C. diff), a serious gut infection.
• Yeast infections - Antibiotics kill good bacteria too. This can lead to vaginal yeast infections. Over-the-counter antifungal creams are safe during pregnancy.
• Allergic reactions - Rash, hives, swelling. True penicillin allergy is rare - only 1-10% of people who think they’re allergic actually are. Many outgrow it. If you think you’re allergic, get tested. Avoiding penicillins unnecessarily means you might get a less safe alternative.

The CDC says 90% of people who report a penicillin allergy can safely take it after proper testing. That’s huge - because penicillins are the safest option. Skipping them just because of an old rash or family history can put you at higher risk.

Why Counseling Matters - And What Good Counseling Looks Like

Most side effects are preventable - if you know what to expect. And many people stop antibiotics early because they feel better. That’s dangerous.

Good counseling includes four key points:

1. Why you need it - Untreated UTIs can lead to kidney infections, which raise your risk of preterm labor by 50-70%. Untreated bacterial vaginosis? That increases preterm birth risk too.
2. Why this drug is safe - Don’t just say "it’s okay." Say: "Amoxicillin has been studied in over 100,000 pregnancies. No increase in birth defects. It’s the standard for a reason."
3. What side effects to expect - "You might feel a little nauseous on day two. Take it with toast. If diarrhea lasts past two days after finishing, call us."
4. Finish the whole course - Even if you feel fine. Stopping early breeds resistant bacteria. That’s dangerous for you - and for future pregnancies.

A 2021 study of over 1,200 pregnant patients found that when providers gave this kind of detailed counseling, patients were 37% less likely to stop their antibiotics early. They were also 29% more likely to finish the full course. Knowledge reduces fear. Fear leads to non-adherence. Non-adherence leads to complications.

What’s New in 2026 - And What’s Still Missing

The field is changing. In 2023, the FDA started pushing drug companies to include pregnant people in clinical trials. For decades, they were excluded. That left huge gaps in data.

The NICHD launched the Antimicrobial Resistance in Pregnancy (AMRIP) initiative in January 2024. It’s tracking 15,000 pregnancies exposed to antibiotics to see how they affect newborns - especially in the third trimester. That’s the first large-scale effort of its kind.

But here’s the problem: fewer than 30% of antibiotics prescribed during pregnancy have solid human safety data. Newer drugs like tedizolid or delafloxacin? We just don’t know enough. That’s why sticking with the old, well-studied options - amoxicillin, cephalexin, clindamycin - is still the smartest move.

And while the FDA now says fluoroquinolones (like ciprofloxacin) can be used in life-threatening cases, the European Medicines Agency still bans them. That’s a sign of how uncertain the data still is. Until more studies come in, avoid them unless there’s no other option.

Bottom Line: Trust the Evidence, Not the Fear

Getting an infection during pregnancy isn’t something to panic about. But it’s not something to ignore either. The right antibiotic, at the right time, can protect both you and your baby. The safest options - penicillins and cephalosporins - have decades of data behind them. Side effects like nausea or diarrhea are common, but manageable. And stopping antibiotics early? That’s riskier than the drug itself.

If you’re prescribed an antibiotic during pregnancy, ask: "Why this one? Is it the safest choice? What side effects should I watch for? What happens if I don’t take it?" You’re not being difficult - you’re being informed. And that’s exactly what good care looks like.