This paper compares the effects of viewing videos with 2D and 3D displays with regard to the viewing distance (3H vs. 6H, where H is the height of the screen) and viewing time to determine the physical stresses in terms of heart rate variability, galvanic skin resistance (GSR), and performance of the viewer (percent of correct responses). Twenty healthy male university students with a mean age ± standard deviation of 27.7 ± 2.53 years participated in this study as volunteers. None had color blindness, and all had normal vision acuity. Display type by viewing distance interaction had a significant effect on most of the heart rate variability measures and associated with watching time for the GSR responses. The results concluded that viewing the 3D display from a short viewing distance produced significantly high physical stresses compared to viewing the 2D display from the same short viewing distance. However, the 3D display seemed to impart lower physical stress than the 2D display at long viewing distances. The findings of this study indicate that physical stresses appeared significant at close viewing distance after watching a 3D display for 50 min and increased with continued watching time. In addition, viewer performance was higher for the 3D compared to 2D display type.