well did you check the vanity its made of press-wood. caulk the bottom of the toilet so pee-pee from poor aim wont run under the toilet. bleach will nock down the smell. I know when my puppy made pee-pee on the tile floor in the kitchen I would bleach it . the urine would foam up and react with the bleach. good luck
Pee is a common problem in many bathrooms, because as you may know, people tend to pee in them. some people (like myself ;))) dont pee in toilets cuz that is whack as heck, nahmean? I like to pee EVERYWHEERRRE. yup. all over the place. up. down, floor, ceiling, shower, walls. Likely urine has seeped into your walls and is in your house. it is probably breeding. good luck but it will probably destroy your house while you sleep. :((((((( BYE!
Any chance the former owners had cats and that was where the litter box was? It's amazing how some cat odors can permeate things. Even though your replaced the subflooring, some odor could have seeped into your support beams. Other than that, I haven't a clue to your mystery, but I hope you find it out.
Added: How long has the house been empty? My brother just reminded me of an incident when we were kids. One summer our family rented a vacation house (after sitting for months) only to find a horrible smell coming from the toilet. Come to find out, some beastie had crawled into it looking for water and had died (the owner said probably a rat as they put down rat poison during off season). After a few flushes, the remains flushed down the sewer pipe ....but hoo boy, the smell lingered!
So we just bought our house in December and probably two months ago we noticed the awful pee smell coming from the smaller bathroom. It has a toilet, sink, and stand-up shower. No matter how much we cleaned it it still smelled, finally we realized it was the wax seal on the toilet and it needed replaced. Well the floor was ugly so we decided to just change it while we had the toilet up, and it's a good thing we did. After peeling the two layers of vinyl off the floor of course the floor underneath was rotten because it had apparently been leaking for a very long time. So we ripped up all the wood and replaced it all and put new tile down and everything.
Now a couple of weeks after we finished adding the tile the bathroom still has this weird smell that we cannot place. The very bottom of the wall is still exposed because we haven't put new trim back up yet but I put my nose to the floor and smelled all over that bathroom and cannot find the source. I smelled the outside and inside of the toilet, shower, sink, the walls, the floor, and the smell never gets stronger. I don't even know how to explain this smell because it's not like the pee smell from before, it just smells weird. But it is for sure coming from the bathroom. Yes we cleaned the bottom of the toilet before putting it back down. Does anyone have any suggestions as to what the smell is from? It doesn't smell like something died, I really can't place it. Please help!