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The Doctor states several times that he has/had a family.

The episode "The Doctor's Daughter" features Jenny, the Doctor's (cloned) daughter.

In addition, the existence of the Doctor's granddaughter Susan would mean that Susan's mother or father is the Doctor's daughter or son.

In the 9th Doctor's episode "The Doctor Dances", a scientist says something along the lines of, "Before the war, I was both a father and a grandfather. Now I am neither." The Doctor's reply was, "I know the feeling." This incarnation of him also mentioned having a family in the episode "Father's Day".

In another episode, "Fear Her", the 10th Doctor tells Rose that he had kids at some point.

Towards the end of the 11th Doctor's episode, "A Good Man Goes to War", Amy asks the Doctor if he has children, a question he avoids answering.