If you are a man and if you clean the tip of your penis (and urethral meatus – the distal part of the urethra) with iodine or at least soap and water – and if you’ve never had any procedures like a prostate biopsy or a cystoscopy – then your urine should be sterile. Most men don’t get urinary tract infections (UTIs), since the urethra is as long as it is – it’s rare for bacteria to make it very far in through the urethra before the sterile urine washes it out again. Men who’ve had prostate biopsies are a little more prone to UTIs since they may have little channels (fistulas) extending from the rectum into the prostate – where the needle went in to do the biopsy – sometimes these biopsy tracts don’t heal completely.
If you are having your urine tested (a urine analysis – UA), you are given instructions for performing a “Clean Catch UA” or “CCUA” which is basically cleaning as described above (usally using a pre-packaged sanitary towelette), then catching the urine mid-stream in the container. The first couple of ounces that come out wash away any residual bacteria, so the remaining urine should be sterile in the absence of infection.
Since women’s urethras are shorter, they are more prone to UTIs since the bacteria don’t have to travel as far to get to the bladder. Their instructions for performing a CCUA are the same as those for a man. They end up getting them a lot more often, since they are much more prone to bladder infections.
So, in the absence of infection, urine should be not just clean, but sterile. (Except for the first ounce or two that’s peed out, since that may carry some of the bacteria from the distal part of the urethra.You shouldn’t drink urine because it’s so concentrated – for the same reason you shouldn’t drink saltwater – but it wouldn’t hurt you if you did drink a little, as long as you drank some regular water as well to compensate for the solute content.
If you got something toxic in your eyes, however, like battery acid, and if there was no water available, you should flush your eyes with urine. It’s just as safe as water and the tiny amount of bacteria in it won’t hurt anything – it will save your eyes. And unless you’ve just urinated, you’ll always have some with you.