In this letter, thermal analysis results of AlGaN/GaN HEMTs grown on SiC, Si and Sapphire substrates were presented. Accurate channel temperature determination and temperature distribution were carried out using 3-D finite element model for both steady state and transient cases. Present simulation results are in good agreement with experimental data from the literature. Effect of different device parameters such as substrate thickness, gate length, gate width, dissipated power and pulse width were investigated to determine in which range of these parameters GaN-devices provide the best thermal performance. Resulting thermal resistance values have been extracted for different substrates. For single-finger devices grown on Sapphire, Si and SiC substrates, thermal resistances were calculated as follows; 158 degrees C/W, 53.5 degrees C/W and 26.3 degrees C/W, respectively. According to our results, channel temperature is defined as a function of power, gate length, gate width and substrate thickness, for the device grown on SiC that has the best thermal performance. In addition, transient thermal performance was studied for sub micrometer pulse width, and substrate material performances are compared. It is expected that this study facilitates the improvement of AlGaN/GaN HEMTs design to reduce thermal resistance, and also improves the reliability and life-time of these devices.