What Are The Most Common Side Effects of Probiotics? - DrFormulas

Free shipping within USA on orders $75 +. Use code: FREE75 (cannot be combined with other discounts or automatic shipments)

Search our Site

All Topics

What Are The Most Common Side Effects of Probiotics?

Common Side Effects of Probiotics

Most people who take a quality probiotic supplement only notice the positive effects, such as improved digestive functions, a stronger immune system, and a higher level of energy. However, if the good and bad bacteria in your digestive tract are unbalanced, you may notice a few mild side effects of probiotics while your gut is transitioning to a healthier state. Unfortunately, this aspect of taking a probiotic supplement is seldom discussed, which leads some people to conclude that their probiotic supplements are not working as they should. As a result, they stop taking the supplement before they’ve had a chance to reap the benefits. Let’s take a closer look at some of the negative side effects of probiotics and what you can do to reduce or prevent them.

What are the Side Effects of Probiotics?

Mild GI Discomfort

When you begin taking a probiotic supplement, the beneficial bacteria will establish themselves in your gut and start growing. Once their numbers are substantial enough they compete against and reduce the number of bad bacteria. It is during this transition period that you may notice some minor side effects. How long they will last depends on the probiotics you are taking, and how long it takes your system to rebalance.

Side effects of starting probiotics, if they do occur, are usually very mild. When taking a powerful probiotic you may experience: bloating, gas, and mild abdominal discomfort.1

The most commonly noted negative side effect is mild gas and bloating when you initially begin taking probiotics.

After the initial period (within the first few days of taking probiotics), your body should gradually adapt to the new friendly bacteria, allowing for improved digestion. If you are still having discomfort try taking the probiotics on an empty stomach before bed. Probiotics can produce gas when provided with certain kinds of foods and taking probiotics before bed minimizes the chance of that happening.

One other possible side effect is diarrhea or loose stools. That too should pass as your body gets fully adjusted to the new probiotics  In the long run, probiotics should not cause diarrhea. Research shows that probiotics such as Lactobacillus and Saccharomyces boulardii are effective in reducing the duration of diarrhea, particularly cases of diarrhea caused by infections and antibiotics.

Does that mean that probiotics cause constipation? Not necessarily. Constipation is generally more prevalent than diarrhea, affecting about 14 percent of adults in the United States and accounts for around 3.2 million medical visits every year.

Probiotics may actually reduce constipation. According to several studies, probiotics were found to increase the average number of weekly bowel movements by 1.3, and generally supported softer stools that were easier to pass. These studies found Bifidobacterium to be the most effective probiotic for supporting regular digestive health.5

It’s also important to understand that not all probiotics are created equal, meaning that no two probiotic strains will necessarily have the same benefits or side effects. For instance, if one strain of Lactobacillus supports better digestive health, that does not inherently mean that a different strain of Lactobacillus (or a completely different probiotic, like Saccharomyces boulardii) will have the same effect.


Headaches are an uncommon side effect of probiotic supplements. They may be experienced when consuming probiotic-rich foods such as yogurt, kimchi, and sauerkraut, contain biogenic amines, which are substances that naturally form in any protein-based foods as they age or ferment.3 Common amines found in probiotic rich foods include histamine, tyramine, and tryptamine.4 Studies suggest that some people may be sensitive to amines, which can stimualte the central nervous system and potentially cause headaches.5

Maintaining a food diary can help you determine if fermented foods are causing these headaches. Thankfully, even if you do get headaches, you can still take probiotics in the form of supplements instead of through probiotic-rich foods to decrease the amount biogenic amines and heavy seasoning, both of which can cause headaches.

Ways to Reduce the Side Effects of Probiotics

If you are taking a probiotic and are noticing any of the aforementioned side effects, don’t give up on your probiotic supplement. There are things you can do to reduce these minor side effects:

  • Decrease the dosage: If you’re having some discomfort, try reducing the dosage by half. Once the symptoms have disappeared, you can gradually increase the dosage to a higher level.
  • Take on an empty stomach: We recommend taking probiotics 30 minutes before you eat to maximize survival and effectiveness of your probiotic. If you’re still having issues taking probiotics 30 minutes before meals try taking it on an empty stomach before bed.
  • Stay hydrated: The side effects, such as bloating, gas, and mild abdominal cramps, are all happening as your body is detoxifying. Drinking plenty of water will help with the process while preventing you from becoming dehydrated.
  • Be patient: You should give your body at least a week or two to adjust to the beneficial bacteria regaining control of your digestive system. It will be worth it in the end.

Contraindications for Probiotics

 Side Effects of Probioitcs

Although probiotics benefit the immune system, they can potentially pose a danger to people with compromised immune systems because some probiotics may in theory overstimulate the immune system or interrupt certain metabolic pathways.6 Immunocompromised people include those who suffer from an immune-compromising disorder such as untreated HIV. People with weakened immune systems also include those being treated for cancer, people who have had recent bowel surgery, or those that are taking immunosuppressant drugs such as corticosteroids.7

If you have a weakened immune system you should consult your physician before taking a probiotic supplement.


Most people lack good probiotics due to an unbalanced diet filled with processed and refined foods. Therefore, many have opted to add probiotic supplements into their diet.

Side effects may be not noticeable at all if you are taking a low-quality probiotic without live cultures. Others may cause mild stomach upset, gas, bloating, and in rare cases, diarrhea. When choosing a probiotic supplement, remember to look for the “three D’s” to make sure you are getting the best and highest-quality probiotic.

DrFormulas® is a physician-founded health and nutrition company. We are experts in digestive health and take a holistic approach to modern health utilizing the best of traditional, Western, Eastern, and cutting edge medicine. We offer a wide range of digestive supplements to help support a healthier you!


  1. https://nccih.nih.gov/health/probiotics/introduction.htm
  2. https://medlineplus.gov/ency/article/003883.htm
  3. https://www.ncbi.nlm.nih.gov/pubmed/10421978
  4. https://www.healthline.com/nutrition/probiotics-side-effects
  5. https://www.health.harvard.edu/blog/probiotics-may-ease-constipation-201408217377
  6. http://www.berkeleywellness.com/supplements/other-supplements/article/probiotics-pros-and-cons
  7. http://www.aafp.org/afp/2008/1101/p1073.html

Leave a comment

Please note, comments must be approved before they are published