Side Effects of Taking Probiotics

Probiotics are considered to be very safe dietary supplements with many beneficial health effects. However, when taken in large amounts and in very strong concentrations, and especially by children, older people, pregnant women or people with a compromised immune system, they may have a few unwanted effects.

Read below to learn about the most important side effects of taking probiotics and if you have any doubts about your medical condition, always consult your doctor before taking them.

If Taken in Large Amounts Probiotics May Cause Infections

Young Woman Having Cold

Excessive quantities of live bacteria contained in probiotic supplements can in some cases over colonize the intestinal flora, causing headaches and infections, which need to be treated with antibiotics or other medicines. This may be of particular concern to people with a seriously weakened immune system, as well as newborns and elderly persons.

Listed below are some of the most common infections that probiotics may eventually cause.

  • Fungal infections – There have been a few case reports of serious fungal infections that have occurred after the use of probiotics. However, these infections mostly concerned people with a compromised immune system.
  • Gastrointestinal infections – These infections usually attack people that already have a weak immune system as a result of a disease, and which consequently have greater chances of developing intestinal disorders and infections after taking probiotics.
    Symptoms of intestinal infections may include bloated stomach, fever, skin rash, diarrhea, etc.
  • Bacterial Endocarditis – A few cases of bacterial endocarditis (infection of the inner lining of the heart chambers and valves) have been reported after the use of probiotics.

Probiotics May in Some Cases Over Stimulate the Immune System

Young Sick Woman in Bed

High doses and elevated concentrations of probiotics may in some cases cause changes in normal metabolic processes and autoimmune responses of the body.

Probiotics contain live organisms, which may alter the intestinal flora, especially when the body mistakes them for unfriendly, infectious bacteria. This often occurs in people with autoimmune diseases or with an overactive and overaggressive immune system, which does not attack only invading organisms, but also the body itself.

With this in mind, immuno-compromised people should be very careful when taking probiotics, for in these cases probiotics may over stimulate the immune system, cause unhealthy metabolic activities and lead to serious health disorders.

Digestive Problems Caused by Probiotics

Side effects of probiotics in healthy people are very rare, but if they occur, they are usually associated with digestive problems.

In general, probiotics will have very beneficial and positive effects on the intestinal flora, especially when it comes to treating different gastrointestinal disturbances. However, if these effects appear uncomfortable, unpleasant or potentially harmful, the dosage and the use of probiotics should be reduced or stopped.

In most cases digestive side effects of probiotics are caused by the biological adjustment of live bacteria in the body’s intestinal flora or by excessive amounts of these bacteria, and they are usually mild and temporary.

However, these side effects may include gastrointestinal discomforts in the form of flatulence, stomachache, constipation or diarrhea. Some people may even experience metabolic changes, such as malabsorption of food nutrients, weight gain or weight loss.

Have you experienced any of the above mentioned side effects of taking probiotics? Let us know and leave a comment below. It may help other readers who are experiencing similar reactions.

About the author


Jessica is a translator who has lived for many years in Asia and South America. She now lives and works in Europe, while preparing her new journeys. She enjoys traveling, meeting new people, exploring different cultures and foods, and being in love.


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  • Well, Im SO glad I read your article so now I know I am not crazy. After taking this normally fabulous probiotic, I have all the symptoms of a Gastrointestinal infection suddenly. I had no idea that people w Hashimotos (autoimmune issues) should not take this stuff.

    • Taking probiotic suplimement created a lot of digestive problems for me. My whole mouth is full with blisters, gums are swollen and so tender that I can’t even brush. My lips are swollen with tiny pimples on and around. I had a severe case of diareah as well.

  • So what are some safe pro biotic brands for people with hyperactive immunities? And what are the strands of probiotics to avoid? I’ve had an almost impossible time searching for weeks trying to find one that’s “safe”…

  • Well..I will say this, probiotics have helped me with ongoing sinus issues that I have had for 8 months. I was struggling with postnasal drip, earaches, stuffy nose, sore throat, headaches. I started off taking a weak probiotic. It seemed to be working OK. Next, I bought a better probiotic from a health food store. I noticed a good difference. I was getting occasional heartburn which I didn’t think much of. Then I had bought the same brand but maximum strength. My sinus issues went away. The constantly swallowing, earaches, postnasal drip, and everything else cleared up! Finally I was relieved! I was on these ones for 38 days and a total of 3 months of probiotics. Once starting the maximum strength I was burping so much. After every swallow. Even water. I was getting heartburn after I ate anything. Apples, bananas, stomach would hurt after I ate. I would become sick to my stomach. My anxiety and depression was through the roof. I decided to stop the probiotic. Right now I am on day 5 of no probiotic. My heartburn, depression, anxiety, burping, and upset stomach has stopped! Unfortunately, sinus issues are coming back. Hopefully my sinuses don’t get as bad as they were but I don’t think that the probiotic was worth the side effects. That would be a tough call. My mother takes them and her side effects is runny stools. She may have more but it is hard to tell when she takes other medications too.

  • I’ve always had digestive problems ever since I was a kid, and someone told me about how probiotics can help so I asked a friend of mine who is a nurse which probiotics would be good for me. She reported with a list and I did my research on each finding the one I thought most fit my needs. I took them as directed and within days I fell so sick with horrendous stomach and back pains, bloating, constipation and diarrhea, vometting and weight loss from not eating! This has been constant for about 3months..I’ve seen many drs and they all say it’s this and that and prescribe me whatever to make me better but nothing is working. I’m reading this page and wondering if this might finally be my answer? How would I begin to talk to my dr about this and what kind of tests could they soo to diagnose it correctly once and for all? And what are the treatment plans? PLEASE I’m so desperate, can anyone help