I'm sure some parents will invoke the inevitable "you're not a parent you can't understand," but if you find your 16-year-old with a box of condoms you should be thrilled, not alarmed. Having sex at that age is pretty much normal. Not universal, but, you know, common. Not out of the ordinary. As a parent your concern should be about 1) pregnancy, 2) disease, and 3) potential for various emotional and physical traumas. #3 you can't do all that much about, and can happen whether or not your kid is intending to have sex, so that leaves #1 and #2 which...condoms hopefully take care of.
