Recent increased usage of stereo displays has been accompanied by public concern about potential adverse effects associated with prolonged viewing of stereo imagery. There are numerous potential sources of adverse effects, but we focused on how vergence-accommodation conflicts in stereo displays affect visual discomfort and fatigue. In one experiment, we examined the effect of viewing distance on discomfort and fatigue. We found that conflicts of a given dioptric value were slightly less comfortable at far than at near distance. In a second experiment, we examined the effect of the sign of the vergence-accommodation conflict on discomfort and fatigue. We found that negative conflicts (stereo content behind the screen) are less comfortable at far distances and that positive conflicts (content in front of screen) are less comfortable at near distances. In a third experiment, we measured phoria and the zone of clear single binocular vision, which are clinical measurements commonly associated with correcting refractive error. Those measurements predicted susceptibility to discomfort in the first two experiments. We discuss the relevance of these findings for a wide variety of situations including the viewing of mobile devices, desktop displays, television, and cinema.