The way I did was by first pushing the button on the garage motor (that stays in learn mode for about 30 sec), then press and hold the button you want to use on your homelink until the garage motor light flickers. You might have to press and hold the button on the garage opener, but try it without first.

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X5 E53 3.0 built 6/20/04 w/ 19" Sport Pkg Wheels.