The upper Court (F) was the part of the temple that suffered most severely at the hands of the Christian monks. It has been closed to visitors for more than a year for reconstruction. It includes a small vestibule leading to one of the few altars (C) to come down to us from antiquity on their original sites, and to a sacrificial hall (H) with reliefs adorning the walls. At the back of the court are a number of small recesses, some larger than others, and the central recess leads into the sanctuary itself which was cut directly into the cliff backing the temple. The granite portal forming the entrance dates from the time of the Ptolemies. The Sanctuary (I) comprises three chambers. The first two have vaulted ceilings and adjoining recesses. In the first chamber is a scene (on the upper reaches of the right-hand wall) of Hatshepsut, Thutmose III and their little daughter, Princess Ranofru, sacrificing to the barge of Amon. Behind them are the queen's father Thutmose I with his wife Ahmose and their little daughter Bitnofru. A similar scene, somewhat damaged, is represented on
the left-hand wall with Thutmose III kneeling. In the inner room of the sanctuary the reliefs show a marked deterioration from the worthy representations in the reign of Hatschepsut. This room was restored by Euergetes II.
As already mentioned, Hatshepsut's mummy was never found. It was neither in the tomb she constructed in the Valley of the Kings, nor in the one excavated south of the mortuary temple, nor in the shaft at Deir el Bahri, nor in the tomb of Amenhotep II , the 'Safety Tomb' . Whether she was poisoned that Thutmose III might take over the throne, stabbed by her lover, killed by officials jealous of Senmut's favor, or died a natural death remains a matter for speculation.