This paper presents the automatic alignment measuring system for improving the accuracy and working time of alignment of large vertical hydraulic pump turbine. It is general practice that rotating shaft should run within acceptable vibration limit. In order to obtain better run-out data of multi-stage rotor, careful and accurate alignment approach must be established. Generally, present alignment procedure are required several iterative works and so many manpower. Therefore, the new system has been developed using a vector calculation algorithm, laser sensor and data acquisition devices. As a result of appling to actual machines, it is confirmed that manpower is saved up to an average 90%.