When the noun innuendo was first used in English in the early sixteenth century, it was a legal term used to introduce a parenthetical explanation of a reference. Around the 1670s, it started to mean "indirect suggestion" in general, and right around that time it was also used in an inappropriate sense. The word comes directly from Latin, which literally meant "by nodding", because nodding is like referencing something. That's the ablative of innuendum, which was the gerund of the verb innuere, meaning "to nod to" (or "signify"). Taking it apart, we can identify the prefix in-, here meaning "towards", and the hypothesized Latin verb nuere, which would mean "nod". This is unattested, but almost definitely existed, and is thought to be from the Proto-Indo-European reconstruction new, also "nod". Interestingly enough, the English word nod is probably unrelated to nuere - it's thought to be from Proto-Germanic hnudan, which doesn't have anything to do with the PIE root.
Hello! I'm Adam Aleksic. This year, I graduated from Harvard University with a degree in Government and Linguistics. There, I co-founded the Harvard Undergraduate Linguistics Society and wrote a thesis on Serbo-Croatian language policy, magna cum laude. In addition to etymology, I also really enjoy philosophy, trivia, vexillology, geography, board games, conlanging, art history, and law.