One major difference between American bathrooms and Japanese bathrooms is the toilet.
As you can see from this diagram of a typical Japanese bathroom, the toilet is actually segregated from the rest of the room. Thus, you don't have someone needing to use the toilet and bothering someone else who is taking a bath (which, at least in my opinion, is a better way of arranging things).
Some of the houses and many of the businesses have adapted to western toilets, but many of the houses and some of the businesses still have the Japanese-style toilet. The easiest way to picture one of these is to image a urinal turned sideways and put on the floor then modified slightly. To use the toilet you squat over it.
Also, in homes you will find a pair of slippers just inside the room. You take off the slippers you have on, put those on and do what needs to be done, then come back out and change slippers again. You never wear the toilet-slippers in the regular house.
Some terms for toilets include: benjo (informal term used by men and young boys); gofujo (a term used by women which means "the honorable motion place"); toire or o'toire (the "o" is an honorary prefix) and tearai (or o'tearai).
Oh, on unisex toilets. There are some of those in Japan, along with some toilets that are cleaned by females so you might walk into a restroom and find someone of the opposite sex using it. Generally if a door is closed, though, you knock on it first to see if anyone is inside, and if anyone is they will generally knock back on the door.
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