In recent years, production volume of five axis machining center (5-MC) is increasing. However, processing accuracy of 5-MC are inferior to usual three axis machine tools. Because, the structure of 5-MC is complicate, and have a lot of geometric deviations. Geometric deviation is the geometric error of relationship between each axis of 5-MC and it affect the positioning error of spindle. The valuation method of geometric deviation is standardized. But, setup of standardized method is difficult and requires much time. And these cannot valuate all geometric deviation. In this study, the estimation method that can measure all geometric deviations by one setup is developed. The developed estimation method is based on least-squares estimation of system identification. And, the relevance of the proposed estimation method is verified on the simulation. As the result, geometric deviation is not estimated high accuracy. But, accuracy of 5-MC is increase by calibrated using the estimated geometric deviation.