In a teleoperated system, misalignment between the master and slave manipulators can result from clutching, errors in the kinematic model, and/or sensor errors. This study examines the effects of type and magnitude of misalignment on the performance of the teleoperator. We first characterized the magnitude and direction of orientation misalignment created when clutching and unclutching during use of two surgical robots: the Raven II and the da Vinci Research Kit. We then purposely generated typical misalignments in order to measure the impact of such misalignment on user performance of a peg transfer task with the Raven II. Users were able to compensate for misalignment angles up to approximately 20 degrees in both tool orientation and camera viewpoint misalignment. These results can be used to guide the design and control of teleoperated systems for a variety of applications.