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late 14c., "person entrusted with secrets," from Medieval Latin secretarius "clerk, notary, confidential officer, confidant," a title applied to various confidential officers, noun use of adjective meaning "private, secret, pertaining to private or secret matters" (cf. Latin secretarium "a council-chamber, conclave, consistory"), from Latin secretum "a secret, a hidden thing" (see secret (n.)).
Meaning "person who keeps records, write letters, etc.," originally for a king, first recorded c.1400. As title of ministers presiding over executive departments of state, it is from 1590s. The word also is used in both French and English to mean "a private desk," sometimes in French form secretaire. The South African secretary bird so called (1786) in reference to its crest, which, when smooth, resembles a pen stuck over the ear. Cf. Late Latin silentiarius "privy councilor, 'silentiary," from Latin silentium "a being silent."