I'm sure there are a lot of unknowns about HMDs and general health, but I'll try and chime in about the ones I do know... I'm neither a doctor nor is any of this set in stone, so take this with many grains of salt...
"Don't sit so close to the TV, you'll ruin your eyes" - Our parents in the 80s/90s
There are two aspects to this. First, this is totally true of old CRTs for a couple reasons. Most of the damage comes in the form of the extreme brightness when sitting so close. There is also the more minor fact that CRTs put of a low level of X-Ray radiation, but this is well within safe limits. However, LCDs don't give off radiation and I assume the brightness of the LCDs are adjusted because they are so close so neither of these issues need be concerns for calibrated for OLED/LCD HMDs.
Next is focus. Focusing on things close to you is strenuous on your eyes, the closer the worse it is (try reading a book 1" from your face). However, because of the optics of the lenses most HMDs (Rift included) actually focus out at infinity. Focus-wise it's the same for your eyes as looking really far off in this distance. In this respect the HMD is actually easier on your eyes than a computer monitor that is only a few feet from you. It also means nearsighted people need to either wear glasses or change the lenses in the HMD or everything is out of focus as it would be in the real world.
As far as stereo imagery there are a few concerns. When you look at something the real world your eye's "toe in"/converge to the distance of the object away from you and then focus of the eye is accommodated to this change. There is a direct relationship between the two components. However, with stereo 3D (movies, TV, games and HMDs) the focus remains constant (because the distance of the screen doesn't change like the distance of real world object do) while the other eye factors adjust. This is really simplifying, but it essentially breaks that relationship. As far as I know other than causing eye strain or discomfort, there are no reported long term effects, but there are still a number of people that raise alarms about messing up children's brains/vision...
Specifically with young children there are some legit concerns, only in the sense that the IPD (how far apart your eyes are) is a major factor in the representation and interpretation of stereo images. Most 3D content is made for adults assuming a general IPD, but children have much smaller heads and closer IPDs as a result so all the factors of discomfort and such could be amplified significantly for them. However, in movies and such the 3D effect is generally pretty toned down to mitigate the discomfort that some people feel. In fact console manufactures limit this variable as well to the point where you actually can't set the 3D effect high enough to get proper that has real-world levels of depth. IMO, for HMD's the IPD makes such a huge difference in how well the effect works that I believe this is a setting that should be set for each person in-game, so in an HMD with the lenses at the right distance and the software set correctly this shouldn't be a problem for even children, but for right now young children shouldn't use the Rift for extended periods.
That's the eyeballs, but there is are a lot of higher level psychological and social factors that are unknown. There are obvious things like addiction and such that could come in to play. Another thing we see in the simulator world is what is called the negative transfer of training. This happens when pilots spend so much time on a simulator that is close to feeling real, but not exactly, and because they train their brains so much in the simulator the real world aircraft feels 'wrong' or 'off.' Depending on the training task simulations are sometimes intentionally made to feel very unrealistic to ensure this doesn't happen. There is the possibility (again huge grain of salt!!!) that people that spend too much time in the virtual world may begin to feel strange about the real world. I highly doubt we will see "Inception" levels of effects from this, but there are strange feelings going in and out of the Rift like you are being teleported between worlds in a way that isn't present with books, movies or games.
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