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The eye was a part of the body used for sight.

Some Silurians had a third eye, which could be used for telepathic purposes or as a weapon. (TV: Doctor Who and the Silurians, PROSE: Blood Heat, AUDIO: Bloodtide)

A Dogon's sixth eye allowed someone to look back clearly on their life and make better choices, especially if swallowed. (TV: Random Shoes)

Gallifreyan eyes were better at seeing in the dark, as they could gather and enhance available light. (PROSE: Lucifer Rising) They could also notice incredible amount of detail from distances of at least one hundred yards away, (TV: The Eleventh Hour) as well as people that were well beyond the human line of sight. (TV: The Hungry Earth) Gallifreyans had incredibly precise control of their eyes. (PROSE: Seeing I)

Eyes could be used to tell one's true age; in the case of the Doctor, his human companions found that they could tell, in spite of the differences caused by regeneration, whether incarnations were younger or older by looking into his eyes. Cindy Wu observed through that the Tenth Doctor was older than he looked through his eyes, and as such identified the seemingly older Third Doctor as a younger incarnation. (COMIC: The Lost Dimension) In contrast, River Song could tell that the Tenth Doctor was younger than the succeeding Doctors she was familiar with by looking into his eyes. (TV: Silence in the Library) Despite the advanced age of the War Doctor, Clara Oswald noted that his eyes were younger than those of his future selves in that they were more hopeful. (TV: The Day of the Doctor)

Pigmentation dispersal could cause the eye to change colour. Leela's eye colour changed from brown to blue after the explosion of a Rutan mothership prompted pigmentation dispersal and left her temporarily blind. (TV: Horror of Fang Rock)

Siluriansp80

A Silurian using his third eye. (PROSE: Doctor Who and the Cave-Monsters)

The Master used Chang Lee's human eyes to open the Eye of Harmony in the Doctor's TARDIS (TV: Doctor Who)

After failing to rescue Omega from the black hole he was trapped in, Savar was forced to leave his damaged TARDIS in an escape pod. The I intercepted the pod, taking all relevant technology. However as Time Lord technology utilised retinal verification, they also extracted his eyes. (PROSE: The Infinity Doctors, PROSE: The Infinity Doctors, Seeing I)

Dogon Sixth Eye

A Dogon sixth eye. (TV: Random Shoes)

An Ood's eye colour changed with the level of telepathic activity, normally glowing bright-red but turning to white when not connected to a hive mind. Humans, who only knew the Ood in their telepathy-disabled form, misinterpreted the presence of red eyes as a disease, known as "red-eye". (TV: Planet of the Ood) Under the control of House, one Ood's eyes glowed green. (TV: The Doctor's Wife)

During the Thousand Year War on Skaro, it was thought that Davros had lost his own eyes. (TV: Genesis of the Daleks, AUDIO: I, Davros) Whilst attempting to trick the Twelfth Doctor into giving up his regeneration energy to save the Daleks, Davros managed to cry and even chose to open his real eyes instead of using his Dalek eye, to the surprise of the Doctor. (TV: The Witch's Familiar)

Miss Quill surgery

Miss Quill had her arn removed. (TV: The Metaphysical Engine, or What Quill Did)

Miss Andrea Quill once required surgery that would penetrate the eyeball. The surgery was required so Quill could have her arn removed to regain her free will. Ballon was responsible for administrating the surgery. He also used his shapeshifting abilities, drawn from the blood of his god, to rebuild the eye to approximately its previous state, leaving behind a long scar down her face. (TV: The Metaphysical Engine, or What Quill Did)

A student in St. Luke's University named Heather was born with a defect, which left her left iris in the shape of a star (TV: The Pilot).

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