GaN layers have been grown by molecular beam epitaxy with a rf plasma source on Al2O3(0001) and 6H-SiC(0001). The conductive n-SiC substrates were employed for the in situ characterization of the grown GaN layers by electron spectroscopies (HREELS and XPS). Transmission electron microscopy (TEM) in the conventional and high-resolution mode provides information regarding the structural properties. Plan-view TEM yields a threading defect density of 7 x 10(9) cm(-2) in GaN/6H-SiC and 2 x 10(10) cm(-2) in GaN/Al2O3. Micro-Raman spectroscopy, by analysis of the coupled A(1)(LO)-phonon-plasmon mode, provides the free carrier concentrations to be n similar to 1-2 X 10(17) cm(-3) for GaN layers grown on both substrates. The in situ HREEL spectroscopy gives insight into the electronic and vibrational properties of the GaN surface. Deep levels at similar to 900 meV above the valence band maximum induce a surface absorption structure which is reduced after heating at 600 degrees C and which might be assigned, according to the growth process and to the literature, to the presence of Ga vacancies in the as-grown layers, in particular in the region close to the surface. Heating the GaN/6H-SiC heterostructures at 900 degrees C causes complete decomposition of the GaN layer.