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In this paper, we propose a new three-dimensional (3-D) measurement method of objects in unknown liquid with a stereo vision system. When applying vision sensors to measuring objects in liquid, light refraction is an important problem. Therefore, we estimate refractive indices of unknown liquids by using images of water surface, restore images that are free from refractive effects of the light, and measure 3-D shapes of objects in liquids in consideration of refractive effects. The effectiveness of the proposed method is shown through experiments.