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The flu shot only prevents respiratory influenza. It does not prevent the gastrointestinal "flu" virus that makes you have GI symptoms like nausea, vomiting, and diarrhea without the cough and respiratory symptoms of influenza. The flu that makes you throw up is not really influenza, it is just an illness that is also caused by a virus or "bug" (called viral gastroenteritis).

True seasonal respiratory influenza, on the other hand, if bad enough (or if you are very young or over 65) is more likely to cause severe complications or even death. The stomach virus usually doesn't result in the same severity, as long as dehydration is controlled by drinking plenty of liquids (and perhaps an occasional sports drink to replenish electrolytes like sodium, potassium, and chloride).

The shots you get for seasonal influenza, and the flu vaccine to prevent the A-H1N1/09 "Swine Flu", are made for protection against respiratory influenza, not for the "stomach flu".

Fun facts: The intestinal flu is not really the flu. It has been incorrectly called that for a long time, but is actually called gastroenteritis and usually is caused by viral infections but might also be bacterial. Influenza (flu) is a respiratory disease that only rarely causes any gastrointestinal symptoms. A very common viral gastroenteritis is what most people call stomach flu, or they also call it Norwalk flu and is caused by a norovirus.

WikiPedia says:

"Norovirus (formerly Norwalk agent) is an RNA virus (taxonomic family Caliciviridae) that causes approximately 90% of epidemic nonbacterial outbreaks of gastroenteritis around the world, and may be responsible for 50% of all foodborne outbreaks of gastroenteritis in the US. Norovirus affects people of all ages. The viruses are transmitted by fecally contaminated food or water, by person-to-person contact,and via aerosolization of the virus and subsequent contamination of surfaces."

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Q: Do flu shots prevent intestinal flu or do they just prevent the cold flu?
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