A system and method for calculating misalignment of a rotational body includes: deriving radial displacement amounts of the rotational body for at least four or more measurement points; selecting three arbitrary points among all the measurement points to calculate a circle; calculating circle values for all the measurement points from the calculated circle; calculating differences between the calculated circle values and the radial displacement amounts as error amounts at the measurement points; summing the error amounts to derive a total error amount value; repeating calculation for combinations of three measurement points to calculate each total error amount value; selecting a calculated circle with a minimum total error amount value as a most probable circle; and calculating deviation between the center of the most probable circle and the center of rotation of the rotational body as misalignment data of the most probable circle.