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The body scanner is not the same as a typical x-ray. There are a few techniques used, either millimeter wave scanners which use non-ionizing radiation, or backscatter x-ray machines which use a significantly lower x-ray exposure which is non-penetrating. Both of them are generally considered safe to use in the typical dosages (don’t live inside them, but passing through to travel is fine) although exactly how safe they are is up to some debate.
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