When you're pregnant and get sick, the last thing you want is to choose between treating an infection and worrying about your baby. Antibiotics can be lifesavers - but not all of them are safe. The good news? Many common antibiotics are well-studied and considered safe during pregnancy. The challenge? Knowing which ones, why they’re safe, and what side effects to watch for.

Which Antibiotics Are Actually Safe During Pregnancy?

Not all antibiotics are created equal when it comes to pregnancy. Some have decades of data showing they don’t harm the baby. Others? Not so much.

The safest bets are penicillins and cephalosporins. Amoxicillin, for example, is used in about 60% of antibiotic prescriptions during pregnancy. It crosses the placenta but doesn’t cause birth defects. Studies tracking over 130,000 pregnancies found no increased risk of major malformations. It’s the go-to for ear infections, sinus infections, and urinary tract infections (UTIs). Ampicillin works the same way.

Cephalosporins like cephalexin (Keflex) are nearly as safe. They’re often used when someone says they’re allergic to penicillin - but here’s the catch: most people who think they’re allergic aren’t. About 90% of those with a reported penicillin allergy can safely take it after proper testing. Skipping penicillin and jumping to a less-studied drug can actually increase risk.

Clindamycin is another trusted option, especially for dental infections or bacterial vaginosis. It reaches the fetus at about 30-40% of maternal levels, but no link to birth defects has been found in multiple studies. It’s also used during labor to prevent Group B Strep transmission.

Nitrofurantoin (Macrobid) is the top choice for simple UTIs in the second and third trimesters. It doesn’t cross the placenta much, so the baby gets very little. But it’s not used in the first trimester - there’s a small increased risk of cleft lip, about 2.4% higher than baseline. And it’s avoided right before delivery because it might interfere with newborn red blood cell function.

What About Metronidazole and Azithromycin?

Metronidazole (Flagyl) is tricky. It’s Category B - meaning no proven risk in humans - but it’s usually avoided in the first trimester. Why? Rodent studies at extremely high doses showed possible DNA damage. But those doses are 50 to 100 times what a pregnant person would ever take. In reality, it’s commonly used after the first trimester for bacterial vaginosis and trichomoniasis. Topical gels (like MetroGel) are even safer - almost no absorption into the bloodstream.

Azithromycin (Zithromax) is now considered one of the safest macrolides. A 2024 update from ACOG reviewed data from over 45,000 pregnancies and found no increase in heart defects or preterm birth. It’s the preferred treatment for chlamydia during pregnancy. But not all macrolides are equal. Erythromycin and clarithromycin have been linked to a rare but serious condition called infantile hypertrophic pyloric stenosis (IHPS), especially when taken in the first trimester. That’s why azithromycin is now the clear winner.

Antibiotics to Avoid - and Why

Some antibiotics should never be used during pregnancy - not even in emergencies - unless there’s no other option.

Tetracyclines - including doxycycline and minocycline - are a hard no after week 5. They bind to developing bones and teeth, causing permanent yellow-gray-brown staining. They can also slow bone growth. Even a single dose can cause damage.

Sulfonamides like Bactrim (sulfamethoxazole-trimethoprim) carry a 2.6-times higher risk of neural tube defects (like spina bifida) if taken in the first trimester. They’re sometimes used later in pregnancy if no alternatives exist, but they’re not first-line.

Aminoglycosides - gentamicin and tobramycin - are Category D. They can cross the placenta and damage the baby’s inner ear, leading to hearing loss. These are only used in life-threatening infections (like sepsis) and only with careful blood monitoring to keep drug levels low.

Fluoroquinolones - like ciprofloxacin and levofloxacin - are banned in Europe during pregnancy. The FDA says they’re not absolutely forbidden but should be avoided unless there’s no other choice. Some studies show no increased risk of joint or muscle problems, but long-term data is still limited. Better to pick something with more evidence.

Common Side Effects - And How to Handle Them

Even safe antibiotics can cause side effects. And when you’re already nauseous from pregnancy, extra stomach upset can feel unbearable.

• Nausea and vomiting - Happens in 15-20% of people taking amoxicillin. Take it with food. Avoid empty stomach.
• Diarrhea - Affects 5-25% depending on the drug. It’s usually mild, but if it lasts more than 48 hours after finishing the course, watch for signs of Clostridioides difficile infection: watery stool, fever, belly cramps. Call your provider.
• Yeast infections - Antibiotics kill good bacteria too. Vaginal yeast infections are common. Over-the-counter antifungal creams (like clotrimazole) are safe during pregnancy.
• Headaches or dizziness - Rare, but possible with clindamycin or metronidazole. Rest and hydrate.

Don’t stop taking the antibiotic just because you feel side effects. Most get better after a few days. If nausea is severe, ask your provider about a different form - like a liquid or extended-release version.

Why Counseling Matters - And What It Should Include

Too often, pregnant people are given a prescription with no explanation. That’s dangerous.

Good counseling answers four key questions:

1. Why are you taking this? - Untreated UTIs can lead to kidney infections, which raise your chance of preterm birth by 50-70%. Untreated Group B Strep can cause pneumonia or sepsis in the newborn. The risk of not treating is often greater than the risk of the drug.
2. Why this antibiotic? - Explain the evidence. “Amoxicillin has been studied in over 100,000 pregnancies and shows no increase in birth defects.”
3. What side effects should you expect? - Tell them when side effects might start (e.g., clarithromycin nausea peaks on day 2-3) and how long they’ll last.
4. Why finish the full course? - Stopping early creates resistant bacteria. It’s not just about this infection - it’s about future ones, for you and your baby.

A 2021 study of 1,247 pregnant patients found that those who got this kind of counseling were 37% less likely to stop their antibiotics early. They also felt more in control.

What’s New in 2026?

Things are changing. For years, pregnant people were excluded from drug trials. That’s changing now.

In January 2024, the NIH launched the Antimicrobial Resistance in Pregnancy (AMRIP) study - tracking 15,000 pregnancies exposed to antibiotics. This will give us real data on third-trimester use and long-term child outcomes.

ACOG updated its 2024 guidelines to reflect new data on azithromycin: no increased risk of heart defects. That means it’s now even more widely recommended.

And the FDA is pushing drug makers to include pregnant women in trials. That’s huge. Right now, 60-70% of antibiotics used in pregnancy lack solid human safety data. We’re starting to fix that.

Final Thoughts

You don’t have to suffer through an infection. You don’t have to guess whether a pill is safe. The science is clear on many antibiotics - penicillins, cephalosporins, clindamycin, azithromycin, and nitrofurantoin (after the first trimester) are all solid choices.

Side effects happen. But they’re usually mild and manageable. The real danger? Not treating an infection.

Ask questions. Demand clear answers. If your provider doesn’t explain why they chose a certain antibiotic, ask for more detail. You’re not being difficult - you’re being smart. And in pregnancy, being informed isn’t optional. It’s essential.