Sorry, I answered this question earlier, but yahoo decided to take a break so it did not get entered here.
The answer to your question has been greatly debated and is still in doubt to many scholars. Below is a bit of information I found for you on the subject.
Introduction
Amenhotep IV – better known as Akhenaten was Egypt’s most profound pharaoh to rule Egypt. He led Egypt in a direction that would tag him “The Heretic Pharaoh.” He brought forth new ideas mainly in religion and art that would leave a lasting impression on the world. Unlike most pharaohs, Akhenaten presented himself in a way that would lead to controversy and would shock the world and his culture. We invite you to take an in-depth look at Akhenaten and discover for yourself the man that would lead Ancient Egypt with much mayhem during his reign and thereafter.
To really understand Akhenaten, you must go back to Tuthmosis IV when the city of Thebes became the main habitat for Egypt. Its foremost god was Aten and was created during this time. Aten was the solitary god set up by Amenhotep IV (Akhenaten) to be the main deity. Amenhotep IV eventually changed his name to Akhenaten. The new name took on the meaning “He who is of service to Aten.”
Family
Akhenaten’s parents were Amenhotep III and Queen Tiy. His wife was Nefertiti who was probably a distant relative. The Couple had six daughters named Ankhesenpaaten, Neferneferuaten-tasharit, Neferneferure, Meketaten, Merytaten, and Sotepenre. Also present in the family are two unknown members in Akhenaten’s family. They are Smenkhkare (successor of Akhenaten) and Tutankhaten who was later renamed Tutankhamen.
The Names of Tutankhamen, Egyptian and English
Heru Ka Nakht Tut-Mesut, Nebty Nefer-hepu Segereh-tawy Sehetep-netjer Nebu, Heru-Nub Wetjes-khau Sehetep-netjeru, Nesu-Bity Nebkheperure, Si-Re, Tutankhamen.
Horus Stong Bull Fitting of Created Forms, He of the Two Ladies Dynamic of Laws who calms the Two Lands and Propriates All the Gods, Golden Horus Who Displays the Regalia, Who Propriates All the Gods, King of Upper and Lower Egypt, Lord of Manifestations of Re, Son of Re, The Living Image of Amun
Tutankhamen's Parentage
Tutankhamen is one of the most famous names from ancient history, so it makes it all the more frustrating how little we actually know about him. Even his origins are sketchy. His original name was Tutankhaten (Tut-ankh-aten: "Living Image of Aten"). He was born in about year 8 or 9 of the reign of Akhenaten, but his parentage is up to debate. There are basically two theories.
The Amenhotep and Tiye theory
According to this school of thought, Akhenaten and his father, (Nebmaatre) Amenhotep III had a signifacant co-regency, and Tutankhaten was the last child of Amenhotep and his great wife, Tiye. So little Tutankhaten was Akhenaten's much younger brother, and Ankhesenpaaten's uncle. Of course, this only applies if there was a co-regency of any significant length. Well, you say, who are the king's parents if there wasn't such a co-regency? Glad you asked.
The Akhenaten and Kiya theory
In this scenario, Tutankhaten is the son of Pharaoh Akhenaten and his secondary wife, Queen Kiya. Kiya may have been a Mittanni princess, sent to marry the King of Egypt to seal a peace agreement. During Akhenaten's reign, she was called the "Greatly Beloved Wife" of the king. What could she have done to have to have be elevated to the King's Favorite? Could she have given the Pharaoh a son, when all his Great Wife, Nefertiti , had given him were daughters? If Kiya and Akhenaten were Tutankhaten's parents, he would have been Ankhesenpaaten's half-brother. But brother-sister marriages were common in Ancient Egyptian royal families.