Transmission electron microscopy (TEM) is an unique technique to perform structural investigations with atomic resolution. In this work we present our studies on structure changes of GaN doped with different rare earth ions (RE) by ion implantation and molecular beam epitaxy (MBE). Due to its wide and direct band gap GaN is an ideal host material for RE ions that have very interesting optical properties. Changing RE we can obtain luminescence covering the whole visible light spectrum. We present the influence of different doping conditions using each technique on the characteristic stacking faults formation. We take into account different RE and their concentration. For MBE doped layers, we notice that the increase of the RE concentration above a threshold leads to the disruption of the GaN stacking sequences. We investigate the connection of this disruption with possible RE segregation by measuring the local lattice parameter changes by HRTEM. During doping by implantation, typical stacking faults are formed around the projected stopping power. We present their detailed investigation and we analyze their evolution versus implantation dose (10¹⁴-10¹⁶ at/cm²) and energy (150-300 kV).