In this paper we describe how cross-sectional ballistic electron emission microscopy (XBEEM) can be used to measure the Schottky barrier height profile of a GaAs/AlGaAs multi heterostructure in cross-sectional geometry. By recording ballistic electron spectra across the heterostructure with a local resolution in the nm range, it is found that the measured Schottky barrier height profile is smeared out compared to the conduction band profile calculated from the sample growth parameters. We attribute this behavior to lateral band bending effects along the heterojunction. In addition, we have evidence that the barrier height profile is influenced by single impurities in the AlGaAs layers.