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No definitive answer has been given. But a few theories have emerged: 1) The Gallifrey Chronicles implies the Doctor's parents are a Time Lord called Ulysses (Coming from an aborted movie idea), who uses the alias Joyce when researching in San Francisco, and a human time traveller called Penelope Gate.

2)The book "Lungbarrow" cheekily suggests the former companion Leela, and the Time Lord guard Andred are the Doctor's parents.

3)The mysterious woman who spoke to Wilf in "The End of Time" was described as the Doctor's Mother in some newspapers.