The Doctor has always had a complex relationship with the Master. Even when the rest of the Time Lords were still around, it seemed like the Doctor was the only one who could really understand the Master, and vice versa. Though they were each others' arch-nemeses, there was also a certain amount of backhanded respect between them. In The FIve Doctors, the Master said that "a universe without the Doctor is scarcely worth considering."

According to the Master's entry in the Doctor Who Wiki, some secondary continuity sources (novels and the like) suggest they were good friends at the Time Lord Academy, until they had an encounter with Death who wanted the Doctor to serve her—but the Doctor suggested the Master should be her servant instead. "The Doctor said that ever since he had always felt partly responsible for the carnage the Master would later cause."
Source(s):
http://tardis.wikia.com/wiki/The_Master
http://en.wikipedia.org/wiki/Master_(Doctor_Who)

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