The Doctor's children

The Doctor had various children across their many lives.

Known children
One incarnation of the Doctor had thirteen children with his wife "Patience". Susan Foreman's father was the eldest of these children. (PROSE: Cold Fusion) Even though some accounts claimed that Gallifreyans were sterile after Pythia's Curse, (PROSE: Cat's Cradle: Time's Crucible, et. al) the Curator claimed otherwise when he said one of Susan Foreman's parents was a child of the Doctor via natural means. (PROSE: The Day of the Doctor)

The Twelfth Doctor stated he took the daughter of the President of the High Council away from Gallifrey with him, (TV: Hell Bent) with A Brief History of Time Lords claiming that Susan had been this daughter. Therefore, one of the Doctor's children would have been President at that him. (PROSE: A Brief History of Time Lords)

In the aftermath of the Last Great Time War, the Tenth Doctor stated he had lost of his children in the fighting. A new daughter, Jenny, was artificially created from his DNA through a progenation machine. The Doctor was reminded of all the children he had lost "a long time ago" and ultimately accepted her as his family, only for her to seemingly die in his arms. (TV: The Doctor's Daughter)

"I know. I'm just. When I look at her now, I can see them. The hole they left, all the pain that filled it. I just don't know if I can face that every day."

- The Tenth Doctor talking about his children

Miranda Dawkins was the daughter of the Emperor, a future incarnation of the Doctor, who was later adopted by the Eighth Doctor. (PROSE: Father Time) Edward Grove considered himself a child of the Eighth Doctor because the time paradox he caused when he rescued Charlotte Pollard gave him life. (AUDIO: The Chimes of Midnight)

The Sapling was a sapling of the Planting who was infused with some of the memories of the Eleventh Doctor and Alice Obiefune as his "progenitors". (COMIC: The Scream, et al)

References to children
The First Doctor was once asked by Wong Kei-Ying if he had any "sons... or daughters or both?" to which the Doctor replied "you could put it that way. Sons or daughters, or both, yes." (PROSE: The Eleventh Tiger)

In a conversation about family, Liv Chenka asked the Doctor that, if he had a granddaughter, he must have children. The Eighth Doctor confirmed he had "at least one" child. (AUDIO: The Final Hour)

The Ninth Doctor related to Dr. Constantine's remark about having been a father and grandfather in the past, claiming "I know the feeling". (TV: The Empty Child)

The Tenth Doctor told Rose Tyler that he had once been a dad. (TV: Fear Her)

Amy Pond once asked the Eleventh Doctor if he was a parent, though she received no response. (TV: The Beast Below) At Demon's Run Amy again asked the Doctor if he had children, and he replied "No". Amy then asked "Have you ever had children?" He did not answer. (TV: A Good Man Goes to War)

Clara Oswald, a companion of the Twelfth Doctor who was aware of his part in saving Gallifrey, once attempted to convince a group of Cybermen that she was the Doctor, claiming that their children and grandchildren were missing, assumed dead, adding that they also had a non-Gallifreyan daughter created via genetic transfer. (TV: Death in Heaven)

Parallel universes
In a parallel universe, Susan was the daughter of the Doctor's daughter. (AUDIO: Auld Mortality)