Growth of pendeo-epitaxial (PE) layers introduces misorientation between the seed layers and the overgrown wing layers. The origin of this misorientation has been studied by Transmission Electron Microscopy (TEM) using a set of samples in which subsequent procedures utilized in PE were applied, i.e. growth of GaN template, stripe etching, annealing at the growth temperature of the PE layers and final PE growth. It was shown that etching of seed-stripes did not change the type of defects or their distribution. However, heating to the PE growth temperature drastically modified the surface and V-shaped pits were formed. The surface became smooth again after the PE growth took place. Overgrowth of the V-shaped pits resulted in formation of edge threading dislocations over a seed-stripe region with a dislocation density of 8.0×108 cm−2. Formation of new edge dislocations over the seed can have an influence on the misorientation between the PE grown regions.