The type of protein powder you use will determine the cause of diarrhea from using it. Most protein powders are made from whey, a protein found in cow's milk. If you have a milk allergy, milk intolerance or are lactose intolerant, diarrhea can develop shortly after using protein powder. If you are using a soy-based protein powder, you may have an allergy to soy protein or intolerance. Talk with your doctor for a clinical diagnosis.
Milk Allergy
Milk contains two primary proteins; whey and casein. Whey is commonly used in many protein powders. If you have a known milk allergy, using whey protein powder can cause an allergic reaction that affects your digestive system, respiratory system and your skin. Symptoms of a milk allergy are identifiable because they will cause reactions in other parts of your body aside from your digestive system. Diarrhea, along with bloating, cramping, stomach pain, nausea and vomiting, are common symptoms of a milk allergy. You may also develop hives, shortness of breath and sinus complications after ingesting whey protein powder.
Milk Intolerance
Intolerance to milk differs from a milk allergy because it is caused by the inability of the digestive system to digest the proteins found in milk. A milk allergy is caused by a hypersensitivity of the immune system, not by the digestive system. Children are more prone to have an intolerance to milk proteins, but anyone at any age can develop intolerance. Diarrhea, cramping, bloating and gas occur because your intestine fails to produce the enzyme that is needed to digest whey protein.
Lactose Intolerance
Lactose intolerance is similar to milk intolerance but is caused by an inability to digest the sugar found in milk products. Whey protein powders that are made from milk contain lactose but may not cause symptoms to develop in everyone who is lactose intolerant. Each person can tolerate different amounts of lactose. If you're moderately to severely lactose intolerant, you may develop diarrhea after consuming protein powder. Lactose is a sugar found in milk that is too complex for the body to absorb it. The enzyme lactase is needed to break down lactose into glucose and galactose for proper absorption, according to the National Digestive Diseases Information Clearinghouse.
Soy Considerations
If you're using a soy-based protein powder, you may have a soy allergy or intolerance to the proteins found in soy, notes MayoClinic.com. Soy is a legume, in the same family as peanuts, peas and lentils. If you have a known legume allergy, avoid using all products that contain other legumes until you can be tested for a possible allergy.



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