Abstract A comparative study of GaN grown on sapphire by metalorganic chemical vapor deposition (MOCVD) is performed by transmission electron microscopy (TEM), atomic force microscopy (AFM) and infrared reflectance. A correlation between the microstructure features revealed by TEM/AFM and optical characteristics obtained from infrared reflectance is explored. TEM observations reveal the GaN epilayers with high densities of threading dislocations. Dislocations in the undoped GaN tend to form open core structures, while dislocation lines in the Si-doped GaN are sharper and the strain contrast is much more discrete. Also the GaN buffer layer grown at low temperature is found to transform into the thermodynamically stable wurtzite structure during high temperature post-buffer GaN growth. The infrared reflectance shows the corresponding behavior. The interference fringes of the Si doped sample were observed with the reflectance reduction and contrast damping, which can be interpreted by the presence of a transition/defect layer near the interface of GaN/sapphire.