The purpose of this study was to investigate experimentally, factors determining the navigation accuracy of the MKM navigation system by Zeiss. The MKM consists of an operating microscope mounted to a six-axis motor-driven robot arm and an alpha-workstation. The image-guided surgery device provides navigation information based on calculation of the cartesian coordinates of the robot arm, and coordinates of the focus point assessed by laser assisted measurement. Navigation information (current position, direction and distance to a previously selected target) is optically projected into the microscopic field. Following factors were examined in an experimental setting for their impact on accuracy of the MKM: optical system, mechanical precision of the robot arm, and registration procedure. The robot arm and the optical system of the microscope allow high precision measurements of any focus point (error < 2 mm if the following aspects are considered: the use of auto-focus function instead of manual focusing, positioning of the registration points as a square or a triangle focus point should be selected on a surface that is perpendicular to the optical axis.