The Department of Mutant Affairs was the official government department designed to deal with the issue of mutant activity within the United States, and was headed by Dr. Hank McCoy.
History
X-Men: The Last Stand
Following William Stryker's death at Alkali Lake and the exposure of his crimes against mutant-kind by the X-Men, the US government's Department of Domestic Security and Defense (Stryker's division responsible for dealing with mutant incursions and former mutant weapon division; secretly a front for his mutant experiment programme) was shut down and promptly reformed into the more public Department of Mutant Affairs, with Dr. Hank McCoy taking on the role of Secretary for Mutant Affairs in the President's administration, a role previously assumed by William Stryker.
After reading a magazine on tracking mutations in his office at the Department of Mutant Affairs, Hank McCoy meets with the President and Secretary Trask to discuss the recent revelations surrounding the mutant Leech and the ability of Worthington Labs to reverse engineer a mutant "cure" from his mutation.
Gallery
The logo for the Department of Mutant Affairs, as seen in Hank McCoy's office.