This paper describes a new method of self-calibration for use in step-and-repeat projection aligners. In order to obtain a higher alignment accuracy, it is important to decrease all kinds of stepper fluctuations. In conventional aligners an automatic calibration system, that uses a special reticle for calibration, was proposed. However, the new method uses the usual reticles which have four special small marks on the surrounding region of the device pattern area. Furthermore, only a small detector embedded in the portion of the wafer stage is required for this self-calibration. Therefore, this new system will be implemented easily in any kind of stepper and it can calibrate anytime before exposure. Moreover, the stepper's offsets, such as alignment, focusing, chip rotation and magnification, are all calibrated at the same time. Based on the results, the improvement of the stepper stability is verified in production use level. Moreover, the use of this system for stepper control can also improve stepper through-put.