my son was the same, it's a phase. it does seem like it's more boy than girl associated, because neither of my nieces have done this. it lasted for about 18 months to 2 years, and went in spurts. sometimes, especially during potty training, he would refuse to put anything, including underwear, back on. we eventually decided it wasn't a battle worth fighting, but as long as he had his undies on, we didn't argue with the no clothes thing. he's 7 now, and still prefers to sleep in just underwear, if he gets the choice,and will gladly go without pants or a shirt on weekends when we're just hanging out at the house.
on a somewhat related note, my son has ALWAYS taken all of his clothes off when he poops, and when we're home, or at my mom's, he still does this. if we're at someone else's house, or if he's at school or in public, he knows he can't do that, but he still takes his shoes off to go. the moral here is that it may seem odd to us, but it's totally normal in their eyes, and as long as it doesn't hurt anyone, no reason to fight it!