The methods available for delivering stereoscopic (3D) display using glasses can be classified as time-multiplexing and spatial-multiplexing. With both methods, intrinsic visual artifacts result from the generation of the 3D image pair on a flat panel display device. In the case of the time-multiplexing method, an observer perceives three artifacts: flicker, the Mach-Dvorak effect, and a phantom array. These only occur under certain conditions, with flicker appearing in any conditions, the Mach-Dvorak effect during smooth pursuit eye movements (SPM), and a phantom array during saccadic eye movements (saccade). With spatial-multiplexing, the artifacts are temporal-parallax (due to the interlaced video signal), binocular rivalry, and reduced spatial resolution. These artifacts are considered one of the major impediments to the safety and comfort of 3D display users. In this study, the implications of the artifacts for the safety and comfort are evaluated by examining the psychological changes they cause through subjective symptoms of fatigue and the depth sensation. Physiological changes are also measured as objective responses based on analysis of heart and brain activation by visual artifacts. Further, to understand the characteristics of each artifact and the combined effects of the artifacts, four experimental conditions are developed and tested. The results show that perception of artifacts differs according to the visual environment and the display method. Furthermore visual fatigue and the depth sensation are influenced by the individual characteristics of each artifact. Similarly, heart rate variability and regional cerebral oxygenation changes by perception of artifacts in conditions.