George Atkinson, 13, was with his 11-year-old cousin at the house in Abermorddu, near Wrexham, early Wednesday evening when the accident happened. The rifle pellet lodged in his brain and he was taken to Wrexham's Maelor Hospital where his parents decided late Thurday night to switch off the life support.
John Atkinson, a recently retired police detective sergeant from Pontblyddyn, near Mold, said he and his wife, Jane, had donated the boy's organs.
"It was something he would have wanted" he said. "I'm sure George would be quite prepared to go through with everything we have done. I have already been told today that at least one child received one of George's organs last night."
Mr Atksinson said he knew there was a gun at the house in Abermorddu but insisted he was not blaming anyone for his son's death.
Police are investigating the shooting.