Without denying it completely, Nintendo has stated that there is a "possibility" that games from different regions won't work on the Nintendo 3DS.
In a statement to Eurogamer, the publisher said "Nintendo 3DS hardware is available in three versions: Japanese, American and European/Australian. Nintendo has developed different versions of Nintendo 3DS hardware to take into account different languages, age rating requirements and parental control functionality, as well as to ensure compliance with local laws in each region."
Their recommendation is to purchase software from the proper region. However, it appears that some games might actually work if imported from around the globe.