Several high velocity clouds (HVCs) are now known to be soft X-ray sources. In this paper we suggest that an interaction between the HVCs and the galactic halo is leading to plasma instabilities that generate energetic electrons which in turn generate X-ray emission. This process is essentially analogous to the interaction process between comets and non-magnetized planets with the solar wind which is also known to lead to the generation of X-rays. We show that for reasonable assumptions about the galactic halo magnetic field, the X-ray emission can be converted into an estimate of the mean galactic halo density at the position of the cloud. This provides a method for estimating the baryonic mass of the plasma halo provided that we can obtain a good estimate for the distance to the HVC.