This story appears in the September 2010 issue of National Geographic magazine.

Mummies capture our imaginations and our hearts. Full of secrets and magic, they were once people who lived and loved, just as we do today.

I believe we should honor these ancient dead and let them rest in peace.

There are some secrets of the pharaohs, however, that can be revealed only by studying their mummies. By carrying out CT scans of King Tutankhamun's mummy, we were able in 2005 to show that he did not die from a blow to the head, as many people believed. Our analysis revealed that a hole in the back of his skull had been made during the mummification process. The study also showed that Tutankhamun died when he was only 19—perhaps soon after he suffered a fracture to his left leg. But there are mysteries surrounding Tutankhamun that even a CT scanner cannot reveal. Now we have probed even deeper into his mummy and returned with extraordinary revelations about his life, his birth, and his death.

To me the story of Tutankhamun is like a play whose ending is still being written. The first act of the drama begins in about 1390 B.C., several decades before Tutankhamun's birth, when the great pharaoh Amenhotep III assumes the throne of Egypt. Controlling an empire stretching 1,200 miles from the Euphrates in the north to the Fourth Cataract of the Nile in the south, this king of the 18th dynasty is rich beyond imagining. Along with his powerful queen Tiye, Amenhotep III rules for 37 years, worshipping the gods of his ancestors, above all Amun, while his people prosper and vast wealth flows into the royal coffers from Egypt's foreign holdings.

If Act I is about tradition and stability, Act II is revolt. When Amenhotep III dies, he is succeeded by his second son, Amenhotep IV—a bizarre visionary who turns away from Amun and the other gods of the state pantheon and worships instead a single deity known as the Aten, the disk of the sun. In the fifth year of his reign, he changes his name to Akhenaten—"he who is beneficial to the Aten." He elevates himself to the status of a living god and abandons the traditional religious capital at Thebes, building a great ceremonial city 180 miles to the north, at a place now called Amarna. Here he lives with his great wife, the beautiful Nefertiti, and together they serve as the high priests of the Aten, assisted in their duties by their six cherished daughters. All power and wealth is stripped from the Amun priesthood, and the Aten reigns supreme. The art of this period is also infused with a revolutionary new naturalism; the pharaoh has himself depicted not with an idealized face and youthful, muscular body as were pharaohs before him, but as strangely effeminate, with a potbelly and a thick-lipped, elongated face.

The end of Akhenaten's reign is cloaked in confusion—a scene acted out behind closed curtains. One or possibly two kings rule for short periods of time, either alongside Akhen­aten, after his death, or both. Like many other Egyptologists, I believe the first of these "kings" is actually Nefertiti. The second is a mysterious figure called Smenkhkare, about whom we know almost nothing.

What we know for sure is that when the curtain opens on Act III, the throne is occupied by a young boy: the nine-year-old Tut­ankhaten ("the living image of the Aten"). Within the first two years of his tenure on the throne, he and his wife, Ankhesenpaaten (a daughter of Akhenaten and Nefertiti), abandon Amarna and return to Thebes, reopening the temples and restoring their wealth and glory. They change their names to Tutankhamun and Ankhesenamun, proclaiming their rejection of Akhenaten's heresy and their renewed dedication to the cult of Amun.

Then the curtain falls. Ten years after ascending the throne, Tutankhamun is dead, leaving no heirs to succeed him. He is hastily buried in a small tomb, designed originally for a private person rather than a king. In a backlash against Akhenaten's heresy, his successors manage to delete from history nearly all traces of the Amarna kings, including Tutankhamun.

Ironically, this attempt to erase his memory preserved Tutankhamun for all time. Less than a century after his death, the location of his tomb had been forgotten. Hidden from robbers by structures built directly above, it remained virtually untouched until its discovery in 1922. More than 5,000 artifacts were found inside the tomb. But the archaeological record has so far failed to illuminate the young king's most intimate family relationships. Who were his mother and father? What became of his widow, Ankhesenamun? Are the two mummified fetuses found in his tomb King Tutankhamun's own prematurely born children, or tokens of purity to accompany him into the afterlife?

View Images Icon of ancient Egypt, the teenage pharaoh’s funerary mask immortalizes his features in gold, glass, and semiprecious stones. This and other treasures from his tomb, now in Cairo’s Egyptian Museum, attract a constant swirl of visitors.

View Images Hidden in the desert canyons west of the Nile, the Valley of the Kings holds the tombs of King Tut and his royal relatives. In antiquity this was considered a secluded spot. Today the growing suburbs of Luxor shimmer nearby.

To answer these questions, we decided to analyze Tutankhamun's DNA, along with that of ten other mummies suspected to be members of his immediate family. In the past I had been against genetic studies of royal mummies. The chance of obtaining workable samples while avoiding contamination from modern DNA seemed too small to justify disturbing these sacred remains. But in 2008 several geneticists convinced me that the field had advanced far enough to give us a good chance of getting useful results. We set up two state-of-the-art DNA-sequencing labs, one in the basement of the Egyptian Museum in Cairo and the other at the Faculty of Medicine at Cairo University. The research would be led by Egyptian scientists: Yehia Gad and Somaia Ismail from the National Research Center in Cairo. We also decided to carry out CT scans of all the mummies, under the direction of Ashraf Selim and Sahar Saleem of the Faculty of Medicine at Cairo University. Three international experts served as consultants: Carsten Pusch of the Eberhard Karls University of Tübingen, Germany; Albert Zink of the EURAC-Institute for Mummies and the Iceman in Bolzano, Italy; and Paul Gostner of the Central Hospital Bolzano.

The identities of four of the mummies were known. These included Tutankhamun himself, still in his tomb in the Valley of the Kings, and three mummies on display at the Egyptian Museum: Amenhotep III, and Yuya and Tuyu, the parents of Amenhotep III's great queen, Tiye. Among the unidentified mummies was a male found in a mysterious tomb in the Valley of the Kings known as KV55. Archaeological and textual evidence suggested this mummy was most likely Akhenaten or Smenkhkare.

View Images Mother KV35YL According to DNA tests, this mummy, known as the Younger Lady, is both the full sister of the KV55 mummy—probably Akhenaten—and the mother of his child, Tutankhamun. (Incestuous relationships were not unusual among Egyptian royalty.) History records that Akhenaten married both the famous Nefertiti and a woman named Kiya, but neither of these two women was ever said to be his sister. The Younger Lady is probably one of the five known daughters of Amenhotep III and Tiye.

Our search for Tutankhamun's mother and wife focused on four unidentified females. Two of these, nicknamed the "Elder Lady" and the "Younger Lady," had been discovered in 1898, unwrapped and casually laid on the floor of a side chamber in the tomb of Amenhotep II (KV35), evidently hidden there by priests after the end of the New Kingdom, around 1000 B.C. The other two anonymous females were from a small tomb (KV21) in the Valley of the Kings. The architecture of this tomb suggests a date in the 18th dynasty, and both mummies hold their left fist against their chest in what is generally interpreted as a queenly pose.

Finally, we would attempt to obtain DNA from the fetuses in Tutankhamun's tomb—not a promising prospect given the extremely poor condition of these mummies. But if we succeeded, we might be able to fill in the missing pieces to a royal puzzle extending over five generations.

To obtain workable samples, the geneticists extracted tissue from several different locations in each mummy, always from deep within the bone, where there was no chance the specimen would be contaminated by the DNA of previous archaeologists—or of the Egyptian priests who had performed the mummification. Extreme care was also taken to avoid any contamination by the researchers themselves. After the samples were extracted, the DNA had to be separated from unwanted substances, including the unguents and resins the priests had used to preserve the bodies. Since the embalming material varied with each mummy, so did the steps needed to purify the DNA. In each case the fragile material could be destroyed at every step.

At the center of the study was Tutankh­amun himself. If the extraction and isolation succeeded, his DNA would be captured in a clear liquid solution, ready to be analyzed. To our dismay, however, the initial solutions turned out a murky black. Six months of hard work were required to figure out how to remove the contaminant—some still unidentified product of the mummification process—and obtain a sample ready for amplifying and sequencing.

After we had obtained DNA as well from the three other male mummies in the sample—Yuya, Amenhotep III, and the mysterious KV55—we set out to clarify the identity of Tutankhamun's father. On this critical issue the archaeological record was ambiguous. In several inscriptions from his reign, Tutankhamun refers to Amenhotep III as his father, but this cannot be taken as conclusive, since the term used could also be interpreted to mean "grandfather" or "ancestor." Also, according to the generally accepted chronology, Amenhotep III died about a decade before Tutankhamun was born.

Many scholars believe that his father was instead Akhenaten. Supporting this view is a broken limestone block found near Amarna that bears inscriptions calling both Tutankhaten and Ankhesenpaaten beloved children of the king. Since we know that Ankhesenpaaten was the daughter of Akhenaten, it follows that Tut­ankhaten (later Tutankhamun) was his son. Not all scholars find this evidence convincing, however, and some have argued that Tutankhamun's father was in fact the mysterious Smenkhkare. I always favored Akhenaten myself, but it was only a theory.

Once the mummies' DNA was isolated, it was a fairly simple matter to compare the Y chromosomes of Amenhotep III, KV55, and Tutankhamun and see that they were indeed related. (Related males share the same pattern of DNA in their Y chromosome, since this part of a male's genome is inherited directly from his father.) But to clarify their precise relationship required a more sophisticated kind of genetic fingerprinting. Along the chromosomes in our genomes there are specific known regions where the pattern of DNA letters—the A's, T's, G's, and C's that make up our genetic code—varies greatly between one person and another. These variations amount to different numbers of repeated sequences of the same few letters. Where one person might have a sequence of letters repeated ten times, for instance, another unrelated person might have the same sequence stuttered 15 times, a third person 20, and so on. A match between ten of these highly variable regions is enough for the FBI to conclude that the DNA left at a crime scene and that of a suspect might be one and the same.

Reuniting the members of a family separated 3,300 years ago requires a little less stringency than the standards needed to solve a crime. By comparing just eight of these variable regions, our team was able to establish with a probability of better than 99.99 percent that Amenhotep III was the father of the individual in KV55, who was in turn the father of Tutankhamun.

We now knew we had the body of Tut's father—but we still did not know for certain who he was. Our chief suspects were Akhenaten and Smenkhkare. The KV55 tomb contained a cache of material thought to have been brought by Tutankhamun to Thebes from Amarna, where Akhenaten (and perhaps Smenkhkare) had been buried. Though the coffin's cartouches—oval rings containing the pharaoh's names—had been chiseled off, the coffin bore epithets associated only with Akhenaten himself. But not all the evidence pointed to Akhenaten. Most forensic analyses had concluded that the body inside was that of a man no older than 25—too young to be Akhenaten, who seems to have sired two daughters before beginning his 17-year reign. Most scholars thus suspected the mummy was instead the shadowy pharaoh Smenkhkare.

Now a new witness could be called on to help resolve this mystery. The so-called Elder Lady (KV35EL) mummy is lovely even in death, with long reddish hair falling across her shoulders. A strand of this hair had previously been matched morphologically to a lock of hair buried within a nest of miniature coffins in Tut­ankhamun's tomb, inscribed with the name of Queen Tiye, wife of Amenhotep III—and mother of Akhenaten. By comparing the DNA of the Elder Lady with that from the mummies of Tiye's known parents, Yuya and Tuyu, we confirmed that the Elder Lady was indeed Tiye. Now she could testify whether the KV55 mummy was indeed her son.

Much to our delight, the comparison of their DNA proved the relationship. New CT scans of the KV55 mummy also revealed an age-related degeneration in the spine and osteoarthritis in the knees and legs. It appeared that he had died closer to the age of 40 than 25, as originally thought. With the age discrepancy thus resolved, we could conclude that the KV55 mummy, the son of Amenhotep III and Tiye and the father of Tutankhamun, is almost certainly Akhenaten. (Since we know so little about Smenkhkare, he cannot be completely ruled out.)

Our renewed CT scanning of the mummies also put to rest the notion that the family suffered from some congenital disease, such as Marfan syndrome, that might explain the elongated faces and feminized appearance seen in the art from the Amarna period. No such pathologies were found. Akhenaten's androgynous depiction in the art would seem instead to be a stylistic reflection of his identification with the god Aten, who was both male and female and thus the source of all life.

And what of Tutankhamun's mother? To our surprise, the DNA of the so-called Younger Lady (KV35YL), found lying beside Tiye in the alcove of KV35, matched that of the boy king. More amazing still, her DNA proved that, like Akhenaten, she was the daughter of Amenhotep III and Tiye. Akhenaten had conceived a son with his own sister. Their child would be known as Tutankhamun.

With this discovery, we now know that it is unlikely that either of Akhenaten's known wives, Nefertiti and a second wife named Kiya, was Tutankhamun's mother, since there is no evidence from the historical record that either was his full sister. We know the names of five daughters of Amenhotep III and Tiye, but we will probably never know which of Akhenaten's sisters bore him a child. But to me, knowing her name is less important than the relationship with her brother. Incest was not uncommon among ancient Egyptian royalty. But I believe that in this case, it planted the seed of their son's early death.

View Images Egypt’s head archaeologist, Zahi Hawass (at right) confers with DNA experts after the extraction of bone tissue from one of the mummies found in KV35, a tomb in the Valley of the Kings.

The results of our DNA analysis, published in February in the Journal of the American Medical Association, convinced me that genetics can provide a powerful new tool for enhancing our understanding of Egyptian history, especially when combined with radiological studies of the mummies and insights gleaned from the archaeological record.

Nowhere is this more evident than in our quest to understand the cause of Tutankhamun's death. When we began the new study, Ashraf Selim and his colleagues discovered something previously unnoticed in the CT images of the mummy: Tutankhamun's left foot was clubbed, one toe was missing a bone, and the bones in part of the foot were destroyed by necrosis—literally, "tissue death." Both the clubbed foot and the bone disease would have impeded his ability to walk. Scholars had already noted that 130 partial or whole walking sticks had been found in Tutankhamun's tomb, some of which show clear signs of use.

Some have argued that such staffs were common symbols of power and that the damage to Tutankhamun's foot may have occurred during the mummification process. But our analysis showed that new bone growth had occurred in response to the necrosis, proving the condition was present during his lifetime. And of all the pharaohs, only Tutankhamun is shown seated while performing activities such as shooting an arrow from a bow or using a throw stick. This was not a king who held a staff just as a symbol of power. This was a young man who needed a cane to walk.

Tutankhamun's bone disease was crippling, but on its own would not have been fatal. To look further into possible causes of his death, we tested his mummy for genetic traces of various infectious diseases. I was skeptical that the geneticists would be able to find such evidence—and I was delighted to be proved wrong. Based on the presence of DNA from several strains of a parasite called Plasmodium falciparum, it was evident that Tutankhamun was infected with malaria—indeed, he had contracted the most severe form of the disease multiple times.

Did malaria kill the king? Perhaps. The disease can trigger a fatal immune response in the body, cause circulatory shock, and lead to hemorrhaging, convulsions, coma, and death. As other scientists have pointed out, however, malaria was probably common in the region at the time, and Tutankhamun may have acquired partial immunity to the disease. On the other hand, it may well have weakened his immune system, leaving him more vulnerable to complications that might have followed the unhealed fracture of his leg we evaluated in 2005.

In my view, however, Tutankhamun's health was compromised from the moment he was conceived. His mother and father were full brother and sister. Pharaonic Egypt was not the only society in history to institutionalize royal incest, which can have political advantages. (See "The Risks and Rewards of Royal Incest.") But there can be a dangerous consequence. Married siblings are more likely to pass on twin copies of harmful genes, leaving their children vulnerable to a variety of genetic defects. Tut­ankhamun's malformed foot may have been one such flaw. We suspect he also had a partially cleft palate, another congenital defect. Perhaps he struggled against others until a severe bout of malaria or a leg broken in an accident added one strain too many to a body that could no longer carry the load.

There may be one other poignant testimony to the legacy of royal incest buried with Tutankhamun in his tomb. While the data are still incomplete, our study suggests that one of the mummified fetuses found there is the daughter of Tutankhamun himself, and the other fetus is probably his child as well. So far we have been able to obtain only partial data for the two female mummies from KV21. One of them, KV21A, may well be the infants' mother and thus, Tutankhamun's wife, Ankhesenamun. We know from history that she was the daughter of Akhenaten and Nefertiti, and thus likely her husband's half sister. Another consequence of inbreeding can be children whose genetic defects do not allow them to be brought to term.

So perhaps this is where the play ends, at least for now: with a young king and his queen trying, but failing, to conceive a living heir for the throne of Egypt. Among the many splendid artifacts buried with Tutankhamun is a small ivory-paneled box, carved with a scene of the royal couple. Tutankhamun is leaning on his cane while his wife holds out to him a bunch of flowers. In this and other depictions, they appear serenely in love. The failure of that love to bear fruit ended not just a family but also a dynasty. We know that after Tutankhamun's death, an Egyptian queen, most likely Ankhesenamun, appeals to the king of the Hittites, Egypt's principal enemies, to send a prince to marry her, because "my husband is dead, and I have no son." The Hittite king sends one of his sons, but he dies before reaching Egypt. I believe he was murdered by Horemheb, the commander in chief of Tutankhamun's armies, who eventually takes the throne for himself. But Horemheb too dies childless, leaving the throne to a fellow army commander.

The new pharaoh's name was Ramses I. With him begins another dynasty, one which, under the rule of his grandson Ramses the Great, would see Egypt rise to new heights of imperial power. More than anyone else, this great king would work to erase from history all traces of Akhenaten, Tutankhamun, and the other "heretics" of the Amarna period. With our investigations, we seek to honor them and keep their memories alive.

Since 2001 the Society has supported the research of Zahi Hawass, secretary general of Egypt's Supreme Council of Antiquities and a National Geographic explorer-in-residence. He is the author of Zahi Hawass's Travel Guide to Secret Egypt, forthcoming from National Geographic Books.