There is a possible exception to my statement that the period of separation does not affect your taxes. The exception only applies if you file separately, so it most likely will not apply to you, but I want to mention it just in case. If you file as married filing separately, the question of which one of you can claim the children as dependents will depend on who each child lived with, and for how long. But if you file as married filing jointly, which is the recommended choice, it doesn't matter. You will claim all three children on your joint tax return.
