Old English nacod "nude, unclothed, bare; empty," also "not fully clothed" (a sense still used in 18c.), from Proto-Germanic *nakwadaz (source also of Old Frisian nakad, Middle Dutch naket, Dutch naakt, Old High German nackot, German nackt, Old Norse nökkviðr, Old Swedish nakuþer, Gothic naqaþs "naked"), from PIE root *nogw- "naked" (source also of Sanskrit nagna, Hittite nekumant-, Old Persian *nagna-, Greek gymnos, Latin nudus, Lithuanian nuogas, Old Church Slavonic nagu-, Russian nagoi, Old Irish nocht, Welsh noeth "bare, naked").
Of things, "without the usual or customary covering" (of a sword, etc.), from Old English. Applied to qualities, actions, etc., "mere, pure, open to view, unconcealed," from c. 1200; phrase the naked truth is from early 15c. Phrase naked as a jaybird (1943) was earlier naked as a robin (1879, in a Shropshire context); Middle English had naked as a worm (mid-14c.), naked as a needle (late 14c.). Naked eye "the eye unassisted by any instrument" is from 1660s, an unnecessary term before telescopes and microscopes.