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This has never been specified. Although he has shown signs of having medical knowledge, when asked he has usually stated, in essence, that his a doctor of many things. "The Armageddon Factor" is to date the only story in which it's stated outright that he actually possesses a doctorate, but it's not stated of what, exactly. "The Sound of Drums", "A Good Man Goes to War", and "The Name of the Doctor" have all indicated that the Doctor's use of the name "Doctor" goes far beyond any particular credentials he may or may not hold.