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

When you're pregnant, even a simple infection can feel overwhelming. You don't want to risk your baby’s health, but you also can't ignore a bad urinary tract infection, strep throat, or bacterial vaginosis. The good news? Many antibiotics are safe to use during pregnancy - if you know which ones and how to use them properly. The key isn’t avoiding antibiotics altogether, but choosing the right one at the right time.

Which Antibiotics Are Actually Safe During Pregnancy?

Not all antibiotics are created equal when you're expecting. The safest options have been studied in thousands of pregnancies and show no clear link to birth defects. Penicillins like amoxicillin and ampicillin are the gold standard. They cross the placenta, but decades of data show they don’t increase the risk of major malformations. In fact, amoxicillin is the go-to for Group B Strep during labor and for most common infections like sinusitis or ear infections. Studies tracking over 134,000 pregnancies found no increased risk of birth defects with penicillins.

Cephalosporins like cephalexin and cefaclor are also considered safe and are often used if you’re allergic to penicillin. They work similarly and have the same low-risk profile. For dental infections or bacterial vaginosis, clindamycin is commonly prescribed. It reaches the fetus at about 30-40% of maternal levels, but no consistent evidence links it to harm.

For urinary tract infections (UTIs), which affect nearly half of all pregnant women, nitrofurantoin (Macrobid) is preferred - but only after the first trimester. While there’s a small increased risk of cleft lip if taken early on (about 2.4% absolute increase), studies show no major risks later in pregnancy. It doesn’t cross the placenta much, making it ideal for bladder infections in the second and third trimesters.

Antibiotics to Avoid During Pregnancy

Some antibiotics are outright dangerous. Tetracyclines - including doxycycline and minocycline - are a hard no after the fifth week of pregnancy. They bind to developing bones and teeth, causing permanent gray or yellow-brown staining in your baby’s teeth. They can also slow down bone growth. These are often prescribed for acne or Lyme disease, but if you're pregnant, your doctor will switch you to something else.

Sulfonamides like Bactrim or Septra carry a higher risk in the first trimester. One study found a 2.6-fold increase in neural tube defects when taken early on. They’re sometimes used later in pregnancy if no alternatives exist, but not as a first choice.

Aminoglycosides like gentamicin and tobramycin are used for serious infections, but they can damage your baby’s hearing. These are reserved for life-threatening cases like sepsis, and even then, doctors monitor blood levels closely to keep doses as low as possible.

And then there’s metronidazole (Flagyl). It’s tricky. Animal studies at very high doses raised red flags, so it’s avoided in the first trimester. But for bacterial vaginosis or trichomoniasis in the second and third trimesters, it’s considered safe - and often necessary. Topical gels are even safer, with no systemic absorption.

What Side Effects Should You Watch For?

Even safe antibiotics can cause uncomfortable side effects. The most common? Upset stomach. About 15-20% of people taking amoxicillin feel nauseous. Diarrhea happens in 5-25% of cases, depending on the antibiotic. It’s usually mild, but if it lasts more than 48 hours after finishing the course, it could be Clostridioides difficile (C. diff) - a serious gut infection that needs immediate treatment.

Here’s what helps:

• Take penicillins with food to reduce nausea.
• Stay hydrated - especially if you’re dealing with a UTI.
• Consider a probiotic (like Lactobacillus) to help maintain gut balance, though evidence is mixed.
• Don’t stop the antibiotic just because you feel better. Stopping early increases the risk of the infection coming back - and could lead to antibiotic resistance.

Why Counseling Matters More Than You Think

Many women stop taking antibiotics because they’re scared of side effects or think the infection is gone. But that’s dangerous. Untreated UTIs can lead to kidney infections, which raise your risk of preterm birth by 50-70%. Untreated bacterial vaginosis increases the chance of early labor and low birth weight.

Good counseling changes outcomes. A 2021 study of over 1,200 pregnant women showed that when doctors clearly explained:

• Why the antibiotic was needed,
• What side effects to expect and when,
• Why finishing the full course matters,

…adherence improved by nearly 30%, and unnecessary discontinuation dropped by 37%. Patients who understood the risks of not treating the infection were far more likely to stick with the treatment.

Allergies Are Often Misunderstood

Lots of people say they’re allergic to penicillin. But studies show that 90% of those people aren’t truly allergic. Maybe they had a rash as a kid, or a family member was allergic, or they got sick while taking it and blamed the drug. A real penicillin allergy causes hives, swelling, or trouble breathing - not just an upset stomach.

If you think you’re allergic, ask your doctor about getting tested. It matters because if you’re incorrectly labeled as allergic, you might get a less safe or more expensive antibiotic instead of amoxicillin. That’s especially risky during pregnancy, where alternatives may carry higher risks.

What’s New in 2025?

The field is evolving. In January 2024, the NIH launched the Antimicrobial Resistance in Pregnancy (AMRIP) initiative - a $12.5 million project tracking 15,000 pregnancies exposed to antibiotics. This is the first large-scale effort to study long-term outcomes in babies exposed in utero, especially in the third trimester.

The FDA is also pushing drugmakers to include pregnant women in clinical trials - something that was rare for decades. That means we’ll soon have better data on newer antibiotics like tedizolid and delafloxacin, which currently have little to no safety data in pregnancy.

And azithromycin (Zithromax)? Once questioned for potential heart risks, new data from the Pregnancy Exposure Registry shows no increased risk of cardiac defects. It’s now considered a safe option for chlamydia and other STIs during pregnancy.

What to Do If You’re Prescribed an Antibiotic

Here’s a simple checklist:

1. Ask: “Is this antibiotic proven safe in pregnancy?”
2. Ask: “What’s the risk if I don’t take it?”
3. Ask: “What side effects should I watch for, and when should I call you?”
4. Ask: “Is there a narrower-spectrum option? For example, amoxicillin instead of amoxicillin-clavulanate?”
5. Take it exactly as directed - even if you feel better.

Final Thought: Treating Infection Is Not the Same as Taking Unnecessary Medication

The goal isn’t to avoid antibiotics during pregnancy. It’s to use them wisely. A well-treated infection protects both you and your baby. An untreated one can lead to preterm birth, sepsis, or long-term complications. The safest antibiotic is the one that actually works - and that’s determined by your doctor, your infection, and your medical history.

If you’re unsure, ask for the evidence. Ask for alternatives. Ask for clarification. You have the right to understand why you’re being prescribed something - especially when you’re carrying a baby.