When Western games are released in Japan, it's not uncommon for the more graphic elements to end up on the cutting room floor. Deus Ex: Human Revolution is no exception.
According to Square Enix, the Japanese version will have one cutscene modified because it shows a character's internal organs. In an area of the game, there's a "sexual object", which will be removed in the Japanese version.
These are the two major edits, and Square Enix notes that they fall in line with the Japanese rating agency.
While Japanese movies can be racy and outrageous, Japanese games are subjected to far stricter regulations, because video games and video game consoles have traditionally been sold in toy stores in Japan.