This paper presents a methodology to calibrate kinematic parameters in a Hexapod-type parallel kinematic machine tool. In general, the calibration error of kinematic parameters and the deformation of struts due to the gravity are two major causes of motion errors of a parallel kinematic machine tool. In other words, in order to accurately calibrate kinematic parameters from measured contouring error profiles, it is important to separate the effect of the gravity from them. We propose a calibration method under the cancellation of gravity-induced errors. Experimental comparison shows circularity errors measured in conditions where gravity effect is large are significantly improved by using the proposed calibration method.