CT scans actually have very few, if any side effects. They are much preferable to other forms of imaging (MRI/Traditional X-Rays). The only real risk you run is that of any exposure of radiation, in that it can increase your chances of getting cancer. But with CT's the benefit far outweighs the risk, and the amount of radiation you absorb during the precedure is rather low. The level of radiation your exposed to during a typical scan is about the same amount you'd experiance from just walking around in everyday life over the course of around three years.
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