The microstructure and typical defects in GaN and GaN/GaAlN thin film heterostructures grown on (0001)α-A12O3 were investigated using different transmission electron microscopy (TEM) techniques including diffraction contrast analysis, multiple dark field imaging, and highresolution TEM. The films were grown by metal-organic chemical vapor deposition (MOCVD) technique. All of the films exhibited good electrical/optical properties. Yet, films were found to be of two distinctive types in terms of the microstructure. Films of the first type (A) were found to contain high, up to the 109 cm2, density of inversion domains (IDs) as well as pure edge (b=l/3[11 20]), screw and mixed type dislocations with the average density of 109 - 1010 cm−2. Smoother surface of the film, absence of IDs, and low (down to 107 cm−2 in the device quality layers) density of screw and mixed type dislocations were found to be characteristic for the second type (B) microstructure. The majority of defects present in these B-type GaN and GaN/GaA1N thin films were found to be threading pure edge dislocations associated with low angle tilt sub-grain boundaries. Despite the 1010 cm−2 density of the edge dislocations, the films displayed the devicequality electrical characteristics. Type A and type B microstructure can be obtained by the variation of growth conditions. The correlation between the optical and structural properties are discussed.