Nintendo have responded, in an official statement, to complaints about the 3DS causing users to experience headaches: “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.”
Thanks to MaxConsole for the info.