Auroral X-ray emission was discovered in the 1950s and has been studied with instruments on balloons, rockets and satellites. While this radiation is of prime interest for studies of space plasma in the Earth's magnetosphere the same radiation is also a background for astrophysical observations made during balloon flights at high latitudes. For such observations it is necessary to monitor and understand the properties of this radiation. This is particularly true for hard X-ray polarimetry which is still an observationally unexplored field. Instruments to measure X-ray polarizations are being developed and will probably first be flown on balloons. We discuss how the auroral X-ray emission and in particular its polarization properties may affect these observations and whether these instruments also can provide information about the high energy electrons producing the X-ray aurora. Optical monitoring of the auroral emissions to allow unambiguous relation of X-ray background to aurora is also discussed.