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The head was where the brain was located.
Amy Pond was afraid that travelling in the TARDIS while pregnant would have some sort of effect on the baby, suggesting it could have three heads "or, like, a timehead or something." (TV: Day of the Moon)
The natural design of the 456 consisted of three "heads", connected to one body via three long necks, possibly a conjoined triplet species. It resembled a large, plucked, three-headed swan. (TV: Children of Earth: Day Four)
The people of Harmony kept the living disembodied heads of visitors who were scientifically minded in glass cases to make use of their intelligence. The Second Doctor discovered the room in which the heads were kept during his visit to Harmony. (PROSE: Planet of Bones)