Concerns about potentially harmful effects on the visual system due to the use of head mounted displays (HMDs) in general, and stereoscopic systems in particular, have been raised in the literature. Most of the concerns were based on studies measuring visual function changes following short-term use of HMDs. This study measured functional changes in binocular vision, accommodation, and resolution following 30 min use of HMD in both stereoscopic- and non-stereoscopic modes, and compared them to changes following the same task performed on a desk-top CRT display. No functional differences were found between HMD and CRT and most measured changes were too small to be considered clinically meaningful. An evaluation of subjective comfort found a statistically significant difference in the impression of comfort between the CRT and the HMD in stereoscopic mode, with the latter being less comfortable. It can be concluded that the functional changes reported following short term use of HMDs are not specific to stereoscopic presentation and do not differ from those caused by desk-top CRT display.