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Probiotics and prebiotics are generally considered safe. A few side effects have been reported, including abdominal discomfort and mild to severe flatulence.

Food sources of probiotics are considered more favorable to consumers than supplements because foods offer nutrition as well as the beneficial bacteria contained in probiotics. In addition, probiotic and prebiotic supplements (like all supplements) are not subject to the U.S. Food and Drug Administration (FDA) safety and approval process required for medications. Manufacturers are responsible for ensuring the safety of their supplements, and that their product claims are truthful and not misleading. Furthermore, manufacturers of probiotics and prebiotics are not required to ensure the standardization of active ingredients in these products. The ingredient amounts can vary widely both between different products and product batches. Consumers are advised to carefully check product labels, contact the manufacturer for more information, and consult their physician or registered dietitian before taking any type of dietary supplement.

Probiotics or prebiotics may not be recommended in the following circumstances:

• Immune system deficiency. Anyone with lowered immune system function should consult their physician before consuming any dietary supplements, including probiotics.
  
  
• Gastrointestinal damage. Patients with intestinal damage, especially those recovering from gastrointestinal surgery, or who experience bacterial overgrowth in the intestines, should avoid probiotics.
  
  
• Pregnancy. Women who are pregnant are advised to avoid probiotic supplements. Currently, there is not enough data to determine whether the use of probiotic supplements is safe during pregnancy.
  
  
• Children. Consumers are encouraged to consult their child’s physician before providing probiotic or prebiotic supplements to children under the age of 3 years.