Exactly who Tutankhamun was, and is still a matter of some conjecture. An inscription on one of the great red granite lions from the temple at Soleb refers to Amenhotep Ill as his 'father'. Given that Akhenaten reigned for about 16 years, coupled with the fact that Tutankhamun was about nine years old when he became king, it seems highly implausible that Amenhotep could have been his real father (not to mention that Queen Tiy would have been somewhat old for child-bearing). Rather, it is much more likely that the word 'father' was used very loosely to stress the young king's ideological connections with Amenhotep III and the return to orthodoxy. Thus, Amenhotep III was probably his grandfather, and Akhenaten his father.
This raises another question, because Akhenaten's chief wife Nefertiti was always shown accompanied by daughters, never by a son. The assumption is that another queen atthe court was his mother. One name is particularly prominent at Amarna: that of a lady named Kiya. She certainly seems to have been married to Akhenaten, as one of her titles testifies, 'Greatly Beloved Wife'. Perhaps she was the Mitannian princess Tadukhepa, the daughter of King Tushratta who was given an Egyptian name. She was clearly high in favour before Year 9, but she disappears about Year 11 perhaps this was when Tutankhaten was born and Kiya died in childbirth; damaged mourning scenes in the Amarna royal tomb (room alpha, on Wall F) might support this theory. in earlier reliefs Kiya is shown accompanied by a small daughter possibly Tutankhaten had an eider sister. Many of Kiya's monuments after Year 11 are reinscribed with the name of Akhenaten's eldest daughter, Merytaten, who had succeeded in her mother's role as chief wife after Nefertiti's death.