Prior researches on binocular mismatches of stereoscopic images mostly focus on optical errors (magnification, shift, rotation, distortion) and photometric asymmetries (color, luminance, definition). In this paper, a type of binocular mismatches - effect of absence is investigated to find whether the partial loss of an object in either one of a stereo pair influences characteristics of human fusion and depth perception when certain disparity is provided, in which two situations are taken into account: with overlap and without overlap. Implications for the effect of absence on fusion mechanism and visual comfort are also discussed in this paper. Experimental results prove the conclusion that the effect of absence can cause misperception and contribute to visual discomfort.