I Couldnt get it to work by stock either, but the solution given in this forum post worked.
But, be very careful. This involves registry editing, which can be very dangerous if you get it wrong.
Click on Start button, type
regedit, then click OK. Navigate to the following place in the registry (Windows 7, 64BIT. Should work in most OS's) ...
[HKEY_USERS\S-1-5-21...\Software\Eidos\Deus Ex: HR\Graphics]
StereoMode, setting the value to
You may have to repeat occasionally these steps, the game may reset the value back to 0 if you change any of the gfx settings.