I will be honest with you. After long hours spend playing the 3DS I am having a slight headaches. I solve this issue by just turning down or off the 3D. I will admit though that this is the longest time, in over year or more, that I have spent staring at a DS of any kind. Some of my eye strain could be due to my lack of playing. Here is what Nintendo has to say about the issue.

“We have shown Nintendo 3DS at multiple events around the world to literally hundreds of thousands of people and have received very few negative comments. As with anything that requires focus, from reading to staring at a computer screen, taking breaks frequent breaks is always recommended. When viewing any kind of 3D images (TV, movies etc.), some people might experience minor discomfort. The effects are short term and have no lasting effect, in fact most players can continue after taking a short break. The Nintendo 3D was designed with a 3D depth slider that lets users adjust the 3D effect to a level that suits them for optimum enjoyment.” – Nintendo statement