A combined run-to-run (R2R) and LQG control method has been proposed for rapid thermal processing (RTP) equipment for run-wise improvement and real-time multivariable control of the temperature uniformity over the wafer surface. The standard LQG objective was modified to include a quadratic penalty term for input deviation from bias values which are updated by an R2R control law. The proposed method has been applied to commercial 12- inch rotating RTP equipment with four pyrometers and ten circular groups of tungsten-halogen lamps for measurements and manipulation of wafer temperatures. The performance of LQG control was evaluated under wafer rotation and found to show quite accurate tracking. For evaluation of the combined control technique, a wafer with seven thermocouples (TC’s) attached along the radial direction has been employed for the TC measurements to be used for R2R control, whereas the pyrometer measurements are fed back for real-time LQG control. It was observed that the temperature uniformity is improved as the run number increases.