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Japan is truly a unique country, and one of the aspects that makes it so original is its accommodation system. One of the options that you might have is ryokan, which is a traditional Japanese inn.
Staying in ryokan initially can seem intimidating but it is not that difficult to arrange and could offer you a great deal of insight into a traditional Japanese way of life. With the Internet at hand, it is really easy to book a ryokan. http://www.itcj.or.jp/indexwel.html is a good website which is an association of Japanese inns and another good site is http://www.japaneseguesthouses.com/in... . Both of these sites are easy to navigate and book your trip.
The advantages to staying in ryokans are multifold: it’s truly different to staying in the usual hotels, it is not expensive at all, and if you book a ryokan that is located in the area of hot springs, it can provide truly unforgettable experience of taking a bath in the hot springs (some ryokans even have outside baths).
The most important difference between ryokan and the regular hotel is that guests sleep on the floor on the sleeping mats which for some people is very convenient and comfortable. You can not walk in your shoes in the ryokan, but slippers are provided. That way the place is cleaner, and it actually feels like you are in somebody’s house rather than in a hotel. In your room you will find yukata, which is a Japanese robe similar to kimono (but simpler) which you can put on while you are in the ryokan.
You can also try a Japanese breakfast in your ryokan (it is usually not included in the price – it is about 7-10 dollars per person), and you don’t have to eat it everyday. The food is really unusual and it is definitely not your Western breakfast. It is beautifully presented and very filling.
Some places like Hakone (close to Tokyo and next to Mount Fuji) have ryokans that are built in the area of hot springs. Traveling to Hakone is a good idea for a trip, where you can indulge for a night or two in the stay in the traditional ryokan and take a bath in the hot springs (as often as you want) and have a beautiful and delicious kaiseki-style dinner and breakfast. It is an expensive option but for those who like to try things such as this, it's worth the money.
The prices in the ryokan are per person and can be cheap to very expensive. Remember that you get what you pay for and avoid cheap ryokans if you want a positive experience.