When I wrote our little guide to 3D technology, I included a section on its “dangers.” I decided that about 4 or 5 was about the earliest that should be exposed to 3D content, citing the fact that your visual system is still very much under construction until then. Mark Borchert, an ophthalmologist in LA, seems to agree. That headache and disorientation you get for a bit after a 3D movie are only temporary, it seems.
That said, no one has done any long-term studies yet, so if you’re paranoid, just avoid it. I may defend 3D as a format, but I certainly wouldn’t defend many of the movies coming out these days.