She's been photographed dressed in boys' clothes and with a new short haircut.
To be honest it's a bit sad if the way a three-year-old is dressed sets off a major controversy. But it appears to have done.
An eyewitness told the press: "It's a drastic change. The last time we'd seen her, her hair was longer and blonder, and she was more girlie. We were surprised Angelina dressed her so much like a little boy."
Celebrity stylists have been rushing to comment on the little girl's fashion choices.
Alana Kelen, senior fashion stylist at VH1, told Life & Style: "Shiloh is pushing the boundaries of a tomboy look and crossing over to cross-dresser territory."
"Pushing the boundaries of a tomboy look"?? She's THREE.
Parenting experts have also been lining up to judge Shiloh and her parents.
Glenn Stanton, director of Family Formation Studies at the conservative organisation Focus on the Family, told Life & Style: "Little girls have never been women before. They need help, they need guidance of what that looks like. It's important to teach our children that gender distinction is very healthy."
However others think that Shiloh should be allowed to wear what she likes and work out her own identity.
Parenting coach Karen Deerwester told the magazine: "Giving preschool-age children the freedom and flexibility to experiment with how they want to be seen in the world is a wonderful gift."
Brad Pitt has previously told Oprah Winfrey that Shiloh likes to be called John.
You've got to feel sorry for the kid - would you want your parents going on Oprah and telling the world all their embarassing stories about you?
So what do you think? Should children be allowed to dress how they want?