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According to Clara Oswald in "Death in Heaven" the Doctor has been married at least 4 times that we know of. This list includes River Song (per "The Wedding of River Song", "The Husbands of River Song", et al); Marilyn Monroe (per "A Christmas Carol"; although the Doctor denied the marriage was legitimate, "The Husbands of River Song" established that it apparently counted); Queen Elizabeth I ("The Day of the Doctor"); and a fourth, as yet unconfirmed individual. "The Husbands of River Song" strongly hints that it was Cleopatra. Others have been referenced in novels and other spin-off media. In addition, there was an episode called "The Doctor's Wife" which was about the Doctor's relationship with his TARDIS; the title, however, was meant to be taken metaphorically, not literally in this case.

It should be noted that what constitutes "marriage" varies by legal jurisdiction and by culture. For example, co-habitating with someone of the opposite gender for a period of time is considered "common law marriage" in some places[1]; by that standard a number of the Doctor's companions who took up residence aboard the TARDIS could in theory be considered this[2]. The series has never addressed this question.

  1. Which places recognise common law marriage varies across history.
  2. Although relatively informal, common law marriage does require that both parties consent to the marriage, which would exclude any pairings where there was no such consent. In this context there have in fact been several occasions in which companions have explicitly indicated a desire to stay with the Doctor, including (but not limited to) Rose Tyler ("Army of Ghosts"), Donna Noble ("Journey's End") and Clara Oswald ("Hell Bent") and it is implied that River Song and the Doctor remained together in some fashion for at least 24 years ("The Husbands of River Song").