Methods of calibrating robotic manipulators are disclosed. The present invention uses an inclinometer or a leveling device to provide a reference to calibrate each encoder for each joint of a robotic manipulator. The inclinometer or leveling device is most preferably an electronic protractor or similar device that is placed on a surface of one of the links and the joint is moved until the link is at a preselected angle. In certain embodiments an offset position between the level position and an index position for an absolute encoder is determined and absolute encoder data describing the offset position is recorded. Preferably, the inclinometer is capable of generating a signal that indicates the angle of the surface of the link with respect to the gravity vector. This signal can be used to control the joints and automatically calibrate the manipulator.