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I'm wondering if a 3.3v input to the Pi's GPIO before it is set up will damage that pin.

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I would suggest connecting 3.3V to any MOS device before it is powered up is a bad idea, as it risks reverse biassing the substrate. At the least you should use a series resistor to limit current.

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It is perfectly legal to attach a input to the gpio before it is "setup". Although when plugging in wires it is a good idea to turn off your raspberry pi.

I suggest reading the gpio docs. Here is a pinout diagram of the gpio.

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