Public nudity in Japan is a common, time-honored occurrence in the natural hot spring baths, called onsen. Before individual homes had plumbing, folks would gather at their local onsen to bathe. During the three years I lived in Aomori Prefecture, the northern part of Honshu, Japan's main island, I had the pleasure of visiting dozens of onsen. Let me be clear, since most Americans presumably associate nakedness with sex, onsen going is a highly asexual activity. In fact, it would be extremely rude to gawk or look lustfully at another person's flesh at an onsen. This entry will not interest you if you're looking for a cheap thrill.

How to bathe at an onsen without looking like a gaijin (boorish foreigner):

1. Before leaving home, pack all toiletries and washcloth, preferably in a small, plastic mesh basket, fresh clothes, and a towel.
2. Enter the front door of the onsen and immediately remove your shoes.  Place them on a shelf, then don a pair of provided slippers.
3. Enter into the lobby and proceed to the concierge desk. Pay the concierge, usually between 200-2,000 yen per person (approximately $2.50-$25.00, depending on the current exchange rate). The size and age of the facility, and the variety of baths offered will factor into the cost. An old neighborhood onsen with peeling paint and mold growing in the cracks of tiles would cost 200 yen while bright, spacious, spa-like ones with several baths to choose from and/or with an unparalleled view of the Sea of Japan will cost around 2,000 yen. 
4. Look for the male and female kanji symbols to discern which door to enter to begin your public bathing experience. Few onsen are co-ed and even then, the showers would be separate. If not sure which door, wait until someone goes in or comes out of one of them.
5. Once inside the changing area, remove a small, empty laundry basket from a stack near the door. Find a bench or vacant cubbyhole and remove your clothes - completely - placing them in the laundry basket then putting it in the cubbyhole.
6. Wrap your towel around you, if desired, and grab your plastic basket of toiletries. Locate a stack of tiny, plastic stools. Remove one stool and proceed to the shower area, avoiding direct eye contact with other naked people you encounter.
7. Sit on your stool in front of a shower and scrub yourself thoroughly with soap, wash your hair, brush your teeth, pumice your feet, then do it all over again. You are to make a great show of cleanliness to prove yourself fit to enter the sacred waters. When your skin is almost rubbed raw from your efforts, you are ready to commune with the locals. Leave your washcloth, stool, and plastic basket at your shower station. If your hair is long, put it up.
8. Now choose a bath to enter, if there is more than one, but leave your towel on the side. No fabric may touch the bath water. Baths range from cucumber-cool to molten magma hot. Some are even electrically charged! My favorite baths are outside.
9. Relax. Let the warmth of the mineral-rich water soothe you from the outside in. Stay as long as you like and try all the baths the onsen has to offer.
10. When you're done soaking, get out, grab your towel and go back to your shower station. Rinsing yourself off after your soak is optional, but rinsing the stool you sat on is mandatory.
11. Stack the stool where you found it, collect your plastic basket of toiletries and washcloth and return to your cubbyhole to dress.
12. When you've dressed, stack the laundry basket where you found it and enter the lobby. There, you may partake of a cool, refreshing beverage or ice cream. Make sure you pay the concierge for it. There will be comfy seats, usually a coin-operated massage chair, a few television sets and men sitting around smoking. Stay as long as you like; until your muscles return from that gelatinous state and your mind from nirvana, are able to navigate home.