This paper presents our microscope image stabilization system for in vivo microscopy. This work is a novel robotic application. In vivo microscopy is very in demand due to its potential impact on biological research [1]. However, it has turned out that in vivo microscopy is significantly disturbed by the motion of the imaged tissue of a living animal. The proposed system virtually removes the unwanted motion by synchronizing the motion of the objective lens with it. In order to realize this idea, we have developed a simple contact-type sensor for estimating the motion of organs, and also made a motion compensator for moving the objective lens. Sensing and compensating have been accomplished for 3-D translational motion. Not only laboratory tests with artificial motion, but also in vivo experiments show the successful motion canceling effect of the proposed system.