The Eye of Anubis, commonly called the Millennium Symbol in the anime, only appears when a Millennium Item holder is either using "Shadow Magic," or when someone else is under the control of another Millennium Item. It also appears on all of the Millennium Items, except for the Millennium Key. The Eye of Anubis is an incomplete symbol of the entire Eye of Wdjat, which is only on the Millennium Puzzle out of all the Millennium Items.
In the manga, the Eye of Anubis appeared on Yugi's forehead when he solved the Millennium Puzzle. In the first series anime, it appeared on his shadow. It often appears on Dark Yugi's forehead after he takes control of Yugi or inflicts a Penalty Game.
Several cards feature the symbol. Many cards with the word "Millennium" have the Eye of Anubis in the card artwork. "Millennium Scorpion" has the Eye of Anubis on its back. Many cards that were used by marak and his siblings had the eye of anubis. "Relinkuriboh" appears to have the eye of anubis on it's back.