Nintendo suggests taking short breaks between games.
http://www.nintendoworldreport.com/news/25883
The first cases of headaches caused by the 3DS's 3D display have begun to surface. After hours of play, some players have mentioned that they begin to feel eye strain and headaches. Nintendo suggests players to take breaks between sessions in order to alleviate these issues.
Robert Saunders of Nintendo U.K. notes, "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."
He further elaborates, "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 3DS was designed with a 3D depth slider that lets users adjust the 3D effect to a level that suits them for optimum enjoyment."
Months prior to the release of the handheld, Nintendo released warnings regarding the 3DS's 3D screen, mainly focusing on young children. Several experts, however, have stated that there is no evidence of impairment of vision development in children by 3D displays.
If you need a break from 3D just set the slider to zero, it's not hard.