Where is the mummy?
A wooden box with her cartouche is assigned to the burial of Hatschepsut. The box (see photo below) was discovered in the cache at Deir el-Bahari (DB320) and contains the remains of mummified internal organs (see below). Beyond that Romer found remains of her wooden sarcophagus - beside some objects of other kings - in a pit inside the tomb of Ramesses XI (KV4). Tomb KV4 was apparently used as a workshop for "repairing and sorting" during the "rescue work" on the royal tombs in the times of Pinudjem I (21. dynasty).
The mummy of Hatshepsut has been missing for a long time resp. has not been identified. Thus, several female mummies had been discussed as possibly her body.
Mostly all royal mummies of the kings of the 18. dynasty had been found in the cache at Deir el-Bahari, among them Thutmosis I (the allocation is however questionable), Thutmosis II and III. In addition, the mummy of an unknown woman from the New Kingdom was found next to an empty coffin intended for a woman and the wooden-ivory box shown above (with mummified intestinal organs [perhaps liver or stomach] and the part of a molar). Also this mummy was suspected be that of Hatshepsut.
According to Maspero (Momies Royale; quoted after LAe II, column 1048) the box shown above was re-used in the 21. Dynasty for the burial of the queen Maat-Ka-Ra Mutemhat. Petrie stated (probably following the opinion of Maspero) changes in the cartouche (erasure of the name of Amun) - if so the allocation of content would be uncertain.
However, after a personal inspection N. Reeves contradicts this assumption since he did not discover hints for an alteration of the cartouche (Reeves, N., Valley of the Kings. 1990; Chapter I Notes, 25).
However, it is remarkable that the package [with the visceral organs], that was found in the box is obviously too large for the box and as it prevents the lid from closing properly. Therefore, it is possibly that the package was originally accommodated in another container and does belong to this box. Furthermore, it must be taken into account that the package indicates a re-use of the box in later times.
Furthermore, in the tomb of Amenhotep II (Amenophis II, KV35) several mummies from the 18. dynasty were discovered, among them in a storeroom two women not-identified yet, one called the "Elder Lady" and the other the "Younger Lady" (both are today in the Egyptian Museum, Cairo). It is out of question to identify the "Younger Lady" with Hatshepsut who most likely had become older. The "Elder Lady" who had reached an age of more than 40 years was considered for along time to be - perhaps - queen Tiye (Teje).
Donald Ryan discussed the possibility that the mummy of Hatshepsut had already been found but was not identified to be hers (Ryan, D. P., "Who is buried in KV60", kmt, volume 1, No. 1, 1990). Following the hypothesis of Elizabeth Thomas (Thomas, E., The Royal Necropoleis of Thebes, 1966; cited according to Ryan, kmt 1, 1990). Ryan has proposed that the un-known body found in KV60 might be missing mummy of Hatshepsut.
The Mummy in KV60
Carter discovered tomb KV60 in 1903, however, he closed the robbed and undecorated tomb again after a short inspection. According to Carters report the tomb contained two damaged female mummies, one of it lay in a decorated coffin (KV60-B), the other one on the floor (KV60-A). Beyond that he mentioned in his report some mummified geese.
1906 Edward Ayrton opened KV60 again. Most likely in 1908 he has moved the mummy which was lying in the coffin together with the coffin to the Egyptian Museum at Cairo but there are no records about the removal. The mummy was first registered at the museum in 1916. The coffin was inscribed with the name of Sat-Ra (wr Sdt nfrw nswt In = Great Royal Nurse, In) who had been meanwhile identified as the nurse of Hatshepsut.
The 2nd mummy of a partially unwrapped, fat lady (with huge pendulous breasts) of a middle age with worn off teeth was left in the tomb lying on the floor, as well as the red-blond hairs which lay beneath the bald head (Ryan, 1990). Subsequently, the tomb was closed again.