The problem of visual discomfort caused by watching stereoscopic 3D content must be addressed if 3D movies and TV are to become widespread. Previous research on visual discomfort has mostly relied on subjective assessment methods. Recently, more objective assessment methods for evaluating visual discomfort have been proposed which may avoid the ambiguities of subjective assessment methods. Nevertheless, subjective human factors are also important in analyzing visual discomfort. Thus, it is necessary to correlate objective measures with personal reports from subjects. In this article, the authors measure visual discomfort caused by watching stereoscopic 3D videos by integrating objective and subjective assessment methods with reference to depth and viewing time. To construct an objective assessment method, they detect eye-blinking with near-infrared video and then convert the eye-blinking data to a visual discomfort value by correlating them with the viewer’s discomfort response. The authors use questionnaires as a subjective assessment method of measuring physiological symptoms of visual discomfort. Using both the objective and the subjective assessment results, they then construct a visual discomfort estimation model which includes the parameters of depth and viewing time. Experimental results show that visual discomfort increases as the depth and viewing time increase. In addition, the visual discomfort estimation model shows lower residual errors than those obtained by using separate subjective and objective assessment models.