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The Holy of Holies (Tiberian Hebrew: קֹדֶשׁ הַקֳּדָשִׁים Qṓḏeš HaqQŏḏāšîm) is a term in the Hebrew Bible which refers to the inner sanctuary of the Tabernacle and later the Temple in Jerusalem where the Ark of the Covenant was kept during the First Temple, which could be entered only by the High Priest on Yom Kippur. The Ark of the Covenant is said to have contained the Ten Commandments, which were given by God to Moses on Mount Sinai.
The construction "Holy of Holies" is a literal translation of a Hebrew idiom which is intended to express a superlative. Examples of similar constructions are "servant of servants" (Gen 9:25), "Sabbath of sabbaths" (Ex 31:15), "God of gods" (Deut 10:17), "Vanity of vanities" (Eccl 1:2), "Song of songs" (Song of Songs 1:1), "king of kings" (Ezra 7:12), etc.
In the Authorized King James Version, "Holy of Holies" is always translated as "Most Holy Place". This is in keeping with the intention of the Hebrew idiom to express the utmost degree of holiness. The King James Version of the Bible has been in existence for over four hundred years. For most of that time, it was a primary reference in much of the English speaking world for information about Judaism. Thus, the name "Most Holy Place" was used to refer to the "Holy of Holies" in many English documents.
A related term is the debir (דְּבִיר) transliterated in the Septuagint as dabir (δαβιρ), which either means the back (i.e. western) part of the Sanctuary, or derives from the verb stem D-V-R, "to speak", justifying the translation in the Latin Vulgate as oraculum, from which the traditional English translation "oracle" (KJV, 1611) comes.
The Holy of Holies was hidden by veil, and no one was permitted to enter except the High Priest, and even he could only enter once a year on the Day of Atonement, to offer the blood of sacrifice and incense before the mercy seat. In the wilderness, on the day that the tabernacle was first raised up, the cloud of the Lord covered the tabernacle. There are other times that this was recorded, and instructions were given that the Lord would appear in the cloud upon the mercy seat (kapporet), and at that time the priests should not enter into the tabernacle (Leviticus 16:2). According to the Hebrew Bible, the Holy of Holies contained the Ark of the Covenant with representation of Cherubim. Upon completion of the dedication of the Tabernacle, the Voice of God spoke to Moses "from between the Cherubim". (Numbers 7:89).
The Holy of Holies, the most sacred site in traditional Judaism, is the inner sanctuary within the Tabernacle and Temple in Jerusalem when Solomon's Temple and the Second Temple were standing. The Holy of Holies was located in the westernmost end of the Temple building, being a perfect cube: 20 cubits by 20 cubits by 20 cubits. The inside was in total darkness and contained the Ark of the Covenant, gilded inside and out, in which was placed the Tablets of the Covenant. According to Hebrews 9:4 in the New Testament, Aaron's rod and a pot of manna were also in the ark. The Ark was covered with a lid made of pure gold (Exodus 37:6), known as the "mercy seat" for the Divine Presence.
When the Temple was rebuilt after the Babylonian captivity, the Ark was no longer present in the Holy of Holies; instead, a portion of the floor was raised slightly to indicate the place where it had stood. Josephus records that Pompey profaned the Temple by insisting on entering the Holy of Holies.
The Holy of Holies was entered once a year by the High Priest on the Day of Atonement, to sprinkle the blood of sacrificial animals (a bull offered as atonement for the Priest and his household, and a goat offered as atonement for the people) and offer incense upon the Ark of the Covenant and the mercy seat which sat on top of the ark in the First Temple (the Second Temple had no ark and the blood was sprinkled where the Ark would have been and the incense was left on the Foundation Stone). The animal was sacrificed on the Brazen Altar and the blood was carried into the most holy place. The golden censers were also found in the Most Holy Place.
Traditional Judaism regards the location where the inner sanctuary was originally located, on the Temple Mount in Mount Moriah, as retaining some or all of its original sanctity for use in a future Third Temple. The exact location of the Kodesh Hakodashim is a subject of dispute.
Traditional Judaism regards the Holy of Holies as the place where the presence of God dwells. The Talmud gives detailed descriptions of Temple architecture and layout. According Babylonian Talmud Tractate Yoma, the Kodesh Hakodashim is located in the center North-South but significantly to the West from an East-West perspective, with all the major courtyards and functional areas lying to its east.
The Talmud supplies additional details, and describes the ritual performed by the High Priest. During the ritual, the High Priest would pronounce the Tetragrammaton, the only point according to traditional Judaism that it was pronounced out loud. According to Jewish tradition, the people prostrated themselves fully on the ground when it was said. According to the Talmud, the High Priest's face upon exit from the Holy of Holies was radiant.
While under normal circumstances, access to the Holy of Holies was restricted to the High Priest and only on Yom Kipur, the Talmud suggests that repair crews were allowed inside as needed but were lowered from the upper portion of the room via enclosures so that they only saw the area they were to work on.  
At present it is conjectured that it is located under the Dome of the Rock which stands on the Temple Mount in Jerusalem, though the exact location of the Most Holy Place is not known with absolute certainty. Most Orthodox Jews today completely avoid climbing up to Temple Mount, to prevent them from accidentally stepping on the Most Holy Place or any sanctified areas. A few Orthodox Jewish authorities, following the opinion of the medieval scholar Maimonides, permit Jews to visit parts of the Temple Mount known not to be anywhere near any of the sanctified areas. Orthodox Jewish visitors to the Temple Mount, who come especially from those groups associated with the Temple Institute and its efforts to rebuild a Temple, seek to conform to the minimal requirements for coming near the Temple, such as immersing in a mikvah, not coming during or following menstruation or immediately following a seminal emission, not showing their back towards its presumed location, and other strictures.
To avoid religious conflict, Jewish visitors caught praying or bringing ritual objects are usually expelled from the area by police.
Jewish tradition teaches that when the Third Temple is built, the actual Holy of Holies will be restored. Traditional Judaism regards the location where the inner sanctuary was originally located, on the Temple Mount in Mount Moriah, as retaining some or all of its original sanctity for use in a future Third Temple. The exact location of the Holy of Holies is a subject of dispute.
The Greek New Testament retains the pre-Christian Septuagint phrase "Holy of the Holies" hagios ton hagion (ἁγίος τῶν ἁγίων) without the definite article as "Holy of Holies" hagios hagion (ἁγίος ἁγίων) in Hebrews 9:3. This passed into the Latin Vulgate as Sanctum sanctorum.
Certain branches of Christianity, including the Eastern Orthodox Church, and the Ethiopian Orthodox Church continue to have a tradition of a Holy of Holies which they regard as a most sacred site. The ciborium, a permanent canopy over the altar in some churches, once surrounded by curtains at points in the liturgy, symbolizes the Holy of Holies.
The Greek phrase refers to the Tabernacle or Temple. The name in Greek for the Sanctuary of a Church is Ἱερόν Βῆμα (Hieron Vema, see Bemah), in Russian it is called Святой Алтарь (Svyatoy Altar), and in Romanian it is called Sfântul Altar.
A cognate term in Ge'ez is found in the Ethiopian Orthodox Church: Qidduse Qiddusan, referring to the innermost sanctuary of an Orthodox Christian church, where the tabot is kept and only clergy may enter.
The Saint Thomas Christians (also known as Nasrani or Syrian Christians) from Kerala, South India still follow a lot of Jewish Christian tradition. In Nasrani tradition the Holy of Holies is kept veiled for much of the time. The red veil covers the inner altar or the main altar. It is unveiled only during the central part of the main Nasrani ritual. The main ritual of the Saint Thomas Christians is the Qurbana (derived from the Hebrew word קרבן meaning sacrifice).
The Latin Vulgate Bible translates Qṓḏeš HaqQŏḏāšîm as Sanctum sanctorum (Ex 26:34). Reproducing in Latin the Hebrew construction, the expression is used as a superlative of the neuter adjective sanctum, to mean "a thing most holy". It is used by Roman Catholics to refer to holy objects beyond the Holy of Holies, particularly in religious feast day processions in Southern Germany.
The Vulgate also refers to the Holy of Holies with the plural form Sancta sanctorum (2 Chr 5:7), arguably a synecdoche referring to the holy objects hosted there. This form is also used more broadly in Catholic tradition with reference to sanctuaries other than the Temple in Jerusalem. A notable example is for the Chiesa di San Lorenzo in Palatio ad Sancta Sanctorum, a chapel in the complex of St John Lateran in Rome.
The Salt Lake Temple of The Church of Jesus Christ of Latter-day Saints (LDS) contains a Holy of Holies wherein the Church's President—acting as the Presiding High Priest—enters to fulfill the relationship between the High Priest of Israel and God in accordance with the LDS interpretation of the Book of Exodus (Exodus 25:22) and Mormon religious texts.