For me, the amnio hurt exactly as much as getting 2 shots in the shoulder. Which to me, is not much. Yes the needle is long- but it HAS to be to reach the amniotic fluid. The shot in the belly doesn't hurt any more than any other shot, but the unexpected part was when the geneticist stopped mid-injection and warned me "You will feel another poke when the needle goes through the uterine wall." And lo and behold, I did. It just felt like another small, "internal" shot. Not terribly painful, and no, there was NO pain at the shot site afterward. And it is only in your belly long enough to draw a few vials of fluid- maybe 20 seconds? That part doesn't hurt at all.
They do warn of signs to watch for afterward, like passing unusual amounts of amniotic fluid, or having painful cramps. I think minor cramping would be normal, but nothing painful. Good luck to you, and best wishes for good results. I'm STILL waiting on the final report from my amnio, which was January 10th.
Lisa