The effect of in-situ thermal cycle annealing (TCA) has been investigated for GaN growth on GaAs(lOO), GaAs(111) and sapphire substrates. X-ray diffractometry (XRD) and surface morphology studies were performed for this purpose. Enhanced cubic phase characteristics were observed by employing annealingfor GaN layers grown on (001) GaAs. The thickness of the layer subject to annealing is critical in determining the phase of the subsequently grown layer. Thin initial layers appear to permit maintenance of the cubic phase characteristics shown by the substrate, while hexagonal phase characteristics are manifested for thick initial layers. Higher temperature of annealing of thick pre-annealed layers results in changes from mixed cubic/hexagonal phase to pure hexagonal phase. Growth on GaAs(111) substrates showed single cubic phase characteristics and similar enhancement of crystal quality by using TCA as for layers on GaAs(OOl). Micro-cracks were found to be present after TCA on GaAs(lll) substrates. Thermal cycling also appears to be beneficial for layers grown on sapphire substrates.