Different polarities of heteroepitaxial GaN layers are believed to stem from different growth conditions. It follows then that the difference in structural and electro-optical properties between Ga-or N-polar samples can be assumed to have the same cause. An unintentionally n-type doped GaN layer has been grown exhibiting both polarities on the same, single two-inch sapphire substrate, which allows for a thorough study of the differences between those two polarities. In such a case the growth conditions are the same and thus the variation of all the properties must come from the sample's polarity or its influence on the growth process.Transmission electron microscopy and etching techniques confirm the large variation in morphology across the surface of the sample to be the result of the polarity difference. Wet chemical etching in a mixture of phosphoric and sulfuric acids, as well as photo-electrochemical etching in aqueous KOH solution, reveal very different defect structures for the two polarities. Hall and PL measurements show a large discrepancy in electro-optical properties suggesting preferential impurity incorporation in the N-polar GaN, which is also confirmed by results of SIMS measurements.