Transmission electron microscopy was used for the characterization of GaN epitaxial layers grown by molecular‐beam epitaxy on two different substrates: sapphire (Al2O3) and 6H‐SiC. GaN layers grown on both substrates crystallize with the wurtzite structure. Despite the very different lattice mismatch associated with their two substrates, similar types of defects were formed in the GaN layer; only their density differed. In addition to small‐angle subgrain boundaries two other types of defects were seen in cross‐sectioned samples: defects parallel to the growth surface and microtwins with a width of about 8–10 nm perpendicular to the growth surface. The parallel defects were identified as stacking faults leading to a local fcc atom arrangement in the layer and are believed to be growth defects. The density of these faults decreased with layer thickness. However, the density of the vertical microtwins remained constant through the layer. Slight local lattice twists between the microtwins and surrounding areas or differences of stoichiometry are suggested as an explanation for the observed contrast of the high‐resolution images.