An alignment system for aligning an acetabular cup insertion instrument utilizes pre-operative preferably standing x-rays and intra-operative x-rays to allow the surgeon to compensate for the position of a patient on an operating room table. The system uses a programmable computer connected to a digital x-ray system and an navigation tracking system to provide input for calculating the inclination and anteversion angles of an acetabular cup impactor based on a pre-operative plan developed from the standing x-rays. The system calculates changes in lengths and angles between anatomic landmarks on the pelvis to alter the intra-operative orientation of the acetabular reaming and impacting instruments to produce the desired inclination and anteversion angles when the pelvis is reoriented as the patient is placed on an operating table.