Do Probiotics and Prebiotics Have Side Effects?

December 29, 2025 •

2 min read

While probiotics and prebiotics are widely considered safe for most healthy people, around 18% of people taking probiotics for C. difficile infection experienced some adverse effects like abdominal cramping or nausea. It is important to be aware of the potential side effects and health risks, particularly for vulnerable populations.

Quick Summary

Probiotics and prebiotics can cause temporary digestive discomfort like gas and bloating as the gut adjusts. More serious risks, such as systemic infections, are rare but possible in immunocompromised individuals. It is crucial to understand who is most at risk and how to mitigate potential issues.

Key Points

Initial Discomfort: Mild gas and bloating are the most common initial side effects of both probiotics and prebiotics, typically resolving within a few weeks.
High-Risk Population: Individuals with weakened immune systems, severe illness, or recent surgery face a small but serious risk of infection from probiotics and should only use them under medical supervision.
GI Disorders: People with GI conditions like IBS or SIBO may experience worsened symptoms from prebiotics, which are high in fermentable fibers.
Allergy Considerations: Allergic reactions to supplements are rare and usually caused by additional ingredients like dairy or soy, not the microbes themselves.
Histamine Sensitivity: Some probiotic strains can increase histamine production, potentially causing headaches or allergic-like symptoms in sensitive individuals.
Gradual Start: To minimize digestive side effects, start with a low dose of probiotics or prebiotics and increase gradually over time.

Common Side Effects of Probiotics

Probiotics are live microorganisms beneficial for gut health, but starting them can cause temporary side effects as your body adjusts. These usually fade over time.

Digestive Discomfort

As the gut microbiome changes, digestive issues can occur. These include gas and bloating from carbohydrate fermentation, which can be reduced by starting with a low dose. Changes in bowel movements, such as temporary diarrhea, softer stools, or constipation, have also been reported, particularly with yeast-based probiotics.

Allergic Reactions and Headaches

Allergic reactions are rare and usually linked to non-probiotic ingredients like dairy or soy. Some probiotics or probiotic-rich foods may increase histamine levels, potentially causing headaches in sensitive individuals.

Increased Risk of Infection (High-Risk Groups)

While safe for most, probiotics pose a small, serious infection risk for immunocompromised individuals, those with catheters, recent surgery, or severe acute pancreatitis. Premature infants are also vulnerable.

Potential Side Effects of Prebiotics

Prebiotics, fibers that feed beneficial gut bacteria, are generally safe but can cause digestive issues.

Digestive Issues

Fermentation of prebiotics in the colon can cause gas, bloating, abdominal discomfort, diarrhea, or constipation. Starting with a low dose and increasing gradually can help.

Considerations for Individuals with IBS and SIBO

Prebiotics, often high in fermentable carbohydrates (FODMAPs), can worsen symptoms for those with IBS or SIBO. Individuals with these conditions should be cautious and consult a healthcare provider.

Comparison of Probiotic and Prebiotic Side Effects


Feature	Probiotics	Prebiotics
Mechanism	Introduce new, beneficial live microorganisms.	Provide food for existing beneficial microorganisms.
Common Side Effects	Temporary gas, bloating, diarrhea, constipation, thirst.	Temporary gas, bloating, abdominal discomfort, diarrhea.
Symptom Duration	Usually resolves within a few weeks as the gut adjusts.	Often subsides as the body adapts to increased fiber intake.
High-Risk Population	Immunocompromised, critically ill, premature infants, severe acute pancreatitis.	Individuals with IBS, SIBO, or FODMAP intolerance.
Allergy Risk	Rare, usually due to other ingredients like dairy or soy. Some strains can increase histamine levels.	Extremely rare, often tied to existing intolerance (e.g., fructose) or allergic reaction to source food.

How to Minimize the Risk of Side Effects

Starting with a low dose and gradually increasing it is key for both probiotics and prebiotics to allow your body to adapt. Carefully read labels for potential allergens. While supplements are available, getting probiotics and prebiotics from whole foods is often recommended for healthy adults. Always consult a healthcare professional before starting supplements, especially if you have existing health conditions or are in a high-risk group.

Conclusion

Probiotics and prebiotics are generally safe for most healthy individuals, with common side effects being mild and temporary digestive issues. However, those who are immunocompromised, critically ill, or have certain GI conditions like SIBO or severe IBS should exercise caution and seek medical advice. By understanding the potential risks and taking appropriate steps like starting with a low dose, most people can safely incorporate these into their diet.

World Gastroenterology Organisation Global Guidelines: Probiotics and Prebiotics.

Frequently Asked Questions

Yes, probiotics can cause temporary side effects, most commonly digestive issues like gas, bloating, and diarrhea, especially when you first start taking them. These symptoms often subside within a few weeks as your body adjusts.

Serious risks from probiotics are rare but can occur in vulnerable populations. Critically ill or immunocompromised individuals, those with a central venous catheter, and premature infants are at a higher risk of developing infections and should use probiotics only under medical supervision.

Prebiotics, which are fermentable fibers, can cause digestive side effects such as increased gas, bloating, and abdominal discomfort as they are broken down by gut bacteria. These effects are usually mild and can be managed by starting with a low dose.

Yes, because many prebiotics are high in FODMAPs (fermentable carbohydrates), they can worsen symptoms like gas, bloating, and pain in individuals with Irritable Bowel Syndrome (IBS) or Small Intestinal Bacterial Overgrowth (SIBO).

Individuals with weakened immune systems, those who are critically ill or recovering from major surgery, and premature infants should avoid probiotics unless specifically advised by a healthcare provider. People with severe acute pancreatitis should also not take them.

If you experience mild digestive issues, try starting with a lower dose to allow your gut to adapt. If symptoms persist for more than a few weeks, consider stopping the supplement and consulting a healthcare professional to explore other options.

True allergies to probiotic bacteria are extremely rare. Reactions are more likely to be caused by other ingredients in the supplement, such as dairy, soy, or eggs. It is always wise to check the label for potential allergens.

For most healthy people, obtaining prebiotics from a diverse diet rich in whole foods and probiotics from fermented foods like yogurt or kefir is recommended. This approach supports overall gut health and provides broader nutritional benefits.