Is anything currently connected to the board (apart from the USB cable)?
How did you wire the stepper motor up? Did you use transistors, a driver chip or board or something like that?
http://www.tigoe.net/pcomp/code/circuits/motors/stepper-motors/
If not you may have damaged the Arduino by drawing too much current from it.
I was able to upload to the board and had a stepper motor controller and LCD shields connected.
OK, well more details then. Which motor, which controller, which LCD shield?