Etymology
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mystery (n.1)

early 14c., misterie, in a theological sense, "religious truth via divine revelation, hidden spiritual significance, mystical truth," from Anglo-French *misterie, Old French mistere "secret, mystery, hidden meaning" (Modern French mystère) and directly from Latin mysterium "secret rite, secret worship; a sacrament, a secret thing."

This is from Greek mystērion (usually in plural mysteria) "secret rite or doctrine (known and practiced by certain initiated persons only), consisting of purifications, sacrificial offerings, processions, songs, etc.," from mystēs "one who has been initiated," from myein "to close, shut" (see mute (adj.)); perhaps referring to the lips (in secrecy) or to the eyes (only initiates were allowed to see the sacred rites).

The Greek word was used in Septuagint for "secret counsel of God," translated in Vulgate as sacramentum. Non-theological use in English, "a hidden or secret thing; a fact, matter, etc., of which the meaning explanation, or cause is unknown," is from late 14c. In reference to the ancient rites of Greece, Egypt, etc. it is attested from 1640s. Meaning "detective story" is recorded by 1908. Mystery meat, slang for "unidentifiable meat served in a military mess, student dining hall, etc." is by 1949, probably from World War II armed services.

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mystery (n.2)

"handicraft, trade, art" (archaic), late 14c., misterie, from Medieval Latin misterium, alteration of Latin ministerium "service, occupation, office, ministry" (see ministry), influenced in form by Medieval Latin mysterium (see mystery (n.1)) and in sense by maistrie "mastery." Now perhaps only in mystery play, in reference to the medieval performances, if they often were, as is often said, staged by members of craft guilds. The two senses of mystery formed a common pun in (secular) Tudor theater.

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mystagogue (n.)

"person who initiates into mysteries," 1550s, from Latin mystagogus "a guide to the mysteries," from Greek mystagōgos, from mystēs "one initiated into the mysteries" (see mystery (n.1)) + agōgos "leading, a leader," from agein "to lead" (from PIE root *ag- "to drive, draw out or forth, move"). Related: Mystagogic; mystagogical.

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mystic (adj.)

late 14c., mistike, "spiritually allegorical, pertaining to mysteries of faith," from Old French mistique "mysterious, full of mystery" (14c.), or directly from Latin mysticus "mystical, mystic, of secret rites" (source also of Italian mistico, Spanish mistico), from Greek mystikos "secret, mystic, connected with the mysteries," from mystes "one who has been initiated" (see mystery (n.1)).

Meaning "pertaining to occult practices or ancient religions" is recorded by 1610s. That of "hidden from or obscure to human knowledge or comprehension" is by 1630s.

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mysterious (adj.)

1610s, "full of mystery, obscure, not revealed or explained," from Latin mysterium (see mystery (n.1)) + -ous. Related: Mysteriously; mysteriousness. Earlier in same sense was mysterial (early 15c.), from Late Latin mysterialis.

Mysterious is the most common word for that which is unknown and excites curiosity and perhaps awe; the word is sometimes used where mystic would be more precise. Mystic is especially used of that which has been designed to excite and baffle curiosity, involving meanings in signs, rites, etc., but not with sufficient plainness to be understood by any but the initiated. [Century Dictionary]
God moves in a mysterious way,
His wonders to perform;
He plants his footsteps in the sea,
And rides upon the storm
[Cowper, from the "Olney Hymns," 1779]

Related: Mysteriously; mysteriousness.

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*mei- (2)

Proto-Indo-European root meaning "small."

It forms all or part of: administer; administration; comminute; diminish; meiosis; Menshevik; menu; metier; mince; minestrone; minim; minimum; minister; ministration; ministry; minor; minuend; minuet; minus; minuscule; minute; minutia; Miocene; mis- (2); mite (n.2) "little bit;" mystery (n.2) "handicraft, trade, art;" nimiety.

It is the hypothetical source of/evidence for its existence is provided by: Sanskrit miyate "diminishes, declines;" Greek meion "less, smaller;" Latin minus, minor "smaller," minuere "to diminish, reduce, lessen;" Old English minsian "to diminish;" Russian men'she "less."

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sacrament (n.)

late Old English, in Christian use, "an outward and visible sign of inward and spiritual grace," especially "a sacrament of the Church, one of the religious ceremonies enjoined by Christ or the Church," and later specifically "the sacrament of the Eucharist" (c. 1300), from Old French sacrament "consecration; mystery" (12c., Modern French sacrement) and directly from Latin sacramentum, "a solemn oath" (source also of Spanish sacramento, German Sakrament, etc.), from sacrare "to consecrate" (see sacred).

A Church Latin loan-translation of Greek mysterion (see mystery). The Latin word sacramentum in its secular aspect was used of any engagement or ceremony that binds or imposes obligation, specifically "oath of obedience and fidelity taken by Roman soldiers on enlistment; sum which two parties to a suit first deposit," hence also, "a cause, a civil suit," thus either "a result of consecration" or "a means of consecration." By 3c. it was used in Church Latin for "a mystery, a sacrament, something to be kept sacred; the gospel revelation; a Church sacrament." In theology, particularly, "a solemn religious ceremony enjoined by Christ, or by the church, for the spiritual benefit of the church or of individual Christians, by which their special relation to him is created or recognized or their obligations to him are renewed and ratified."

The meaning "arcane knowledge; a secret; a mystery; a divine mystery" in English is from late 14c. (Wyclif); from mid-14c. as "a solemn oath, pledge, covenant; a ceremony accompanying the taking of an oath or the making of a pledge." The seven sacraments in the West were baptism, penance, confirmation, holy orders, the Eucharist, matrimony, and anointing of the sick (extreme unction); the Reformation loosened the sense in England.

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whodunit (n.)
"murder mystery," 1930, U.S. slang, originally a semi-facetious formation from who done it? Whydunit is from 1968.
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mystique (n.)

1891, "atmosphere of mystery and veneration," from French mystique "a mystic; mystical," from Latin mysticus (see mystic (adj.)).

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spine-chiller (n.)
"mystery film," 1940, from spine + agent noun from chill (v.). Spine-tingler in same sense is from 1942.
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