Your gun WILL be taken, and in many cases, so will all of the rest of your guns (hint: don't put all your eggs in one basket), ammo, mags, and related things in your house.

Depending on how your case goes, and where you are, it may be easy or difficult to get back.  Generally, you won't get the gun from the shooting back until you are officially, and completely, cleared of the shooting.

Of course, there are PLENTY of stories of guns being "lost" while in police custody (i.e., sold out of the evidence room, or now in the sherriff's gun collection), so I'd advise that you don't use any non-replacable gun for self defense.  Grandpa's original 1911 may be a great gun, but it would suck to have it melted down, stolen, or whatever, and even a nice new Kimber wouldn't be the same.

-Troy