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Yes, she is pregnant.

In the original Avatar movie, James Cameron cut out the scene where it showed Neytiri pregnant. In the newly released Special Edition set, the deleted material was added back into it.

At the very end of the Special Edition Disc 2, it shows Neytiri and Jake after the Time of Great Sorrow at a watering hole. Jake says "The forest will heal. New life. It keeps the energy the breath of the world." as he touches Neytiri's abdomen.