This paper proposes a method for the identification of geometric deviations in five-axis machining centers by measurement method based on orthogonal coordinate frame. The ball bar system is used as a measurement instrument. In this method, one rotary axis and two linear axes are simultaneously controlled and the sensitive direction of the ball bar is kept constant in X, Y or Z direction of the machine coordinate accordingly. From the simulated results, it is found that every deviation can be estimated. However, the identification accuracy of this method is affected by installation error of the table side socket.