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)
Jenny was the daughter of the Tenth Doctor who was artificially created from his DNA by a progenation machine. Her creation reminded the Doctor of all the other children he had lost "a long time ago". (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.
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)
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)
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)