Medicine During Pregnancy

There’s a LOT we don’t know about how drugs and treatments affect women and babies during pregnancy. That’s mostly because companies and doctors are (reasonably) scared to study drugs on pregnant women. However, without that information, doctors are basically guessing (see: Thalidomide used to treat morning sickness) and usually don’t know about the long term effects of drugs. 

Safe Medicine During Pregnancy

Here’s what we do know about common medications you might need in pregnancy, and how they could affect the gut bacteria you pass on to your baby.


During pregnancy, your baby grows and starts to squish your stomach, which can lead to acid reflux. 

Doctors treat reflux with PPIs, or proton pump inhibitors. They can be prescribed, or your doctor might recommend an over-the-counter brand like Nexium or Prilosec.

However, studies have consistently shown that acid suppression drugs during pregnancy are linked to an increase in food allergy and asthma in babies.

Why? When PPIs lower stomach acid too much, they may prevent proper digestion of proteins, hurt the lining of the intestines, or kill friendly gut bacteria

If you want to limit use of medications, there are some natural ways you can treat or prevent  acid reflux are:

  • Eat smaller meals more frequently. Your squashed stomach can only fit so much food now.
  • Eat foods that are easier to digest (toast, bananas, eggs) or smoothies that have been blended
  • Eat green leafy vegetables which help reduce stomach acid.
  • Try breathing and yoga poses that help your body create space for the baby
  • Try sleeping slightly elevated to reduce reflux


Antibiotics are life-saving medicines that you should absolutely use if you need them, pregnant or not. Antibiotics work by killing off bacteria that has infected your body and your immune system is unable to kill on its own. Without antibiotics, an infection can spread and hurt your baby. 

The downside of antibiotics is that they can also kill off the healthy, helpful bacteria that keep your skin healthy and your gut working correctly. If you kill off good bacteria, you can also get very sick and send your immune system haywire.

Antibiotics should only be used when they are necessary. Overuse can increase the risk of a baby with allergies.

If you’re pregnant, don’t immediately jump to using antibiotics if you feel sick. If you have a virus, antibiotics won’t help. Talk to your doctor to see if you can wait a couple of days to see if your immune system naturally wins the battle. Some doctors will give you a prescription, but tell you only to fill it if your symptoms keep getting worse. 

Aspirin / Ibuprofen 

Pregnancy is painful. Having your core muscles and rib cage stretched out over 9 months hurts. Many pregnant women desperate for sleep will turn to pain killers. 

There has not been extensive research on how aspirin and ibuprofen affect the risk of food allergy. At least one study showed that frequent use of painkillers does seem to kill friendly gut bacteria, but there isn’t a strong link to allergic disease. 

The best way to deal with the lack of data on how painkillers affect babies is to try to avoid them and use exercise, warm baths, and massage as the first way to treat pain.

Over-the-Counter Cold Remedies

Most over-the-counter cold remedies are really just aspirin. 

Try curing your common cold naturally with humidifiers, more fluids, and rest instead of drugs. 

Remember that cold remedies don’t actually help your body fight off a virus, they simply mask the symptoms. It will take just as long to recover from a cold with or without OTC meds!

Flu Shot and Other Vaccines

Get your flu shot. Having the flu could put you and your baby at serious risk. Better news is that vaccines, like the flu vaccine, have been shown to have no effect on the risk of food allergies.