X-ray topography defect analysis of entire 1.8-inch GaN substrates, using the Borrmann effect, is presented in this paper. The GaN wafers were grown by the ammonothermal method. Borrmann effect topography of anomalous transmission could be applied due to the low defect density of the substrates. It was possible to trace the process and growth history of the GaN crystals in detail from their defect pattern imaged. Microscopic defects such as threading dislocations, but also macroscopic defects, for example dislocation clusters due to preparation insufficiency, traces of facet formation, growth bands, dislocation walls and dislocation bundles, were detected. Influences of seed crystal preparation and process parameters of crystal growth on the formation of the defects are discussed.