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The eye was an organ used for sight.

The eyes of Cybermen were known as eye-pods. (PROSE: Earthshock)

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)

Gallifreyan eyes were noticeably different from human ones. While the human eye was just a dish of light-sensitive cells, leaving the brain to do all of the processing, the Time Lord retina was capable of thinking on its own. (PROSE: Seeing I) They could enhance available light, were thus better at seeing in the dark than human eyes; (PROSE: Lucifer Rising) they could also notice incredible amounts of detail from hundreds of yards away (TV: The Eleventh Hour) and see things beyond the human line of sight. (TV: The Hungry Earth) As a result of these strengths, the retina was the main method of communicating with machines on Gallifrey. (PROSE: Seeing I) The Eighth Doctor's eyes could change colour between green, blue, (PROSE: Vampire Science) and grey, (PROSE: Mad Dogs and Englishmen) and the Master's eyes variously appeared dark blue and dark brown flecked with gold. (PROSE: Doctor Who and the Dæmons) Allisheer St Marx, the half-human daughter of Handramit, had mirror-flecked eyes; (PROSE: Of the City of the Saved...) Antigone's dark eyes were flecked with the tell-tale purple of the Homeworld high-caste. (PROSE: Weapons Grade Snake Oil) One Time Lord advisor's eyes were red pinpricks of light glowing from within darkened sockets, despite his otherwise appearing humanoid. (PROSE: K9 and the Zeta Rescue)

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)

Regeneration could change the colour balance in Time Lords' eyes. (PROSE: 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)

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, Seeing I)

A Dogon sixth eye. (TV: Random Shoes)

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

The Vacant Mitra Ashkanzai stole the eyes of Mae Harrison, and the nose of Natasha. Mrs Harrison walked into heavy traffic, now blind, but made a full recovery. (PROSE: The Pictures of Emptiness)

Dorothy McShane had an eye test when she underwent a full medical examination to be a passenger on the Virgil. (PROSE: At Childhood's End)