Using high resolution electron microscopy, atomistic modelling and image simulations, typical contrast was identified for most of the extended defects which form in epitaxial GaN layers. There are three types of defects which propagate into the active layers: the threading dislocations, prismatic stacking faults and inversion domains. The atomic structure of the a pure edge threading dislocations was shown to exhibit 5/7, or 8 atom cycles. The two configurations were observed at a similar frequency for isolated dislocations and low angle grain boundaries. Coincidence grain boundaries were studied and they were made of pure edge a dislocations with the above identified atomic structures. A topological analysis of high angle grain boundaries was carried out in order to determine the defect content at the interfaces. The reconstruction of some boundaries was only possible by taking into account the occurrence of structural units which exhibit 4 atom ring cycles for the dislocation cores. The {} stacking fault has two atomic configurations in wurtzite (Ga, Al, In)N with 1/2 〈〉 and 1/6 〈〉 displacement vectors. It originates from steps at the SiC surface and it can form on a flat (0001) sapphire surface. The two atomic configurations have comparable energy in AlN, whereas the 1/2 〈〉{} atomic configuration should be more stable in GaN and InN. Observations carried out in plan-view show the 1/2 〈〉{} atomic configuration in GaN layers. The 1/6 〈〉 configuration was found inside the AlN buffer layer in cross section observations. It folds rapidly to the basal plane, and when back into the prismatic plane, it bears the 1/2 〈〉{} atomic configuration. The {} inversion domains in GaN layers grown on sapphire substrate were identified in multi-beam dark field images and by convergent beam electron diffraction. In the investigated samples, Holt and V models are shown to form in samples depending on the growth conditions. The samples containing Holt inversion domains exhibited a flat surface morphology, whereas the V IDBs were observed in the centre of small pyramids (100 nm high) protruding at the sample surface. The Holt inversion domains were always smaller (<20 nm), at quite high densities (2.5 × 1010 cm—2), whereas the V ones could reach 50 nm and one order of magnitude lower density. The inversion domains were found to be generated mostly at sapphire surface steps where they minimized the large misfit along the c axis (20%).