This paper presents a novel modeling and compensation approach for the angular transmission error in harmonic drive gearings. In the modeling, physical phenomena of the transmission error due to nonlinear elastic deformations in micro-displacement region are especially dealt with, as well as the synchronous component which has been discussed in a variety of conventional studies. On the basis of the analyses of the phenomena, the nonlinear elastic component is mathematically modeled by applying a modeling framework for the rolling friction with hysteresis attributes. The proposed transmission error model has been adopted to the positioning system as a model-based feedforward compensation manner. Experimental results using a prototype show the effectiveness of the proposed modeling and compensation. Copyright © 2009 Institute of Electrical Engineers of Japan. Published by John Wiley & Sons, Inc.