The focal point of the Deir el-Bahari complex is the Djeser-Djeseru meaning "the Holy of Holies" of the Mortuary Temple of Hatshepsut. It is a colonnaded structure, which was designed and implemented by Senemut, the superintendent and architect of Hatshepsut (believed by some to be her consort), to serve for her posthumous worship and to honor the glory of Amun.

Djeser-Djeseru sits atop a series of colonnaded terraces, reached by long ramps that once were graced with gardens. It is built into a cliff face that rises sharply above it, and is largely considered to be one of the "incomparable monuments of ancient Egypt.

The unusual form of Hatshepsut's temple is explained by the choice of location, in the valley basin of Deir el-Bahari, surrounded by steep cliffs. It was here, in about 2050 BC, that Mentuhotep II, the founder of the Middle Kingdom, laid out his sloping, terrace-shaped mortuary temple. The pillared galleries at either side of the central ramp of the Djeser Djeseru correspond to the pillar positions on two successive levels of the Temple of Mentuhotep.

Today the terraces of Deir el-Bahari only convey a faint impression of the original intentions of Senenmut. Most of the statue ornaments are missing - the statues of Osiris in front of the pillars of the upper colonnade, the sphinx avenues in front of the court, and the standing, sitting, and kneeling figures of Hatshepsut; these were destroyed in a posthumous condemnation of this pharaoh.