There were ill feelings between both of them for a long time. Later in life Junior said that he didn't know how a father could bring his son into the mob life. Of course this was after Junior had been to prison, seen all the backstabbing in the mob, and was no longer Acting Boss. But he had no complaints years before when he was riding on his father's coat tails.

But it seems they sort of made up towards the end. Junior visited his father in prison not long before Gotti died and, after pressure on Gotti from his wife, he gave Junior the OK to leave the life; something he previously had not been willing to do.