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How can I use the Adafruit Motor HAT and RPI GPIO at the same time? I just need an extra tall stacking header, or there is something I missing?

My goal is use the Motor HAT and some LED and HC-SR04 with it.

See Adafruit DC & Stepper Motor HAT for Raspberry Pi - Mini Kit

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    A bunch of the GPIOs are visibly broken out and labelled #4, #17, etc., on the HAT. You probably want to solder pins or a female header into the holes.
    – goldilocks
    Commented Jun 12, 2017 at 17:28

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I don't think you are missing anything.

The problem is pretty much a mechanical one, how do you connect to GPIO not been used by the HAT.

If the HAT is a permanent addition you could just solder to the pads on the HAT. If not you could use an adapter block with long pins between the Pi and the HAT and connect jumper wires to the pins. Alternatively you could solder wires to the pins on the underside of the Pi.

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