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Why did you decide to go to Japan? You must have something in mind that fascinates you and places you want to visit.

places to visit
Tokyo + Kyoto would be a must for me and with 3 weeks in Japan, I'd spend a minimum of 3 days each. Whatever else you visit will depend on interests. There are plenty of interesting places around Tokyo and Kyoto which could help to keep your transportation costs down.

travel
certainly look into (night) buses for long distance transportation which will help a lot to keep costs low. With the Japan Bus Pass you might even save more, depending on itinerary. For regional travel there exist some passes but which one to get will depend on your itinerary so you'd need to get a better idea of where you want to go first. Don't move around too much if you are on a tight budget.

accommodation
typical hostel fare is 3000 yen, budget hostels (only exist in a few places such as Tokyo, Kyoto) from around 2000 yen and apparently there are some extreme budget places (likely sub-Japanese standard, but might work for you) from 1000 yen or so in Osaka.

Some useful resources to help you decide on where to go:

1) thorn tree forum has plenty of sample itineraries
2) Japan Guide
3) JNTO
4) Your guidebook
5) a picture guidebook such as eyewitness guide
6) movies, documentaries,... on Japan

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Thank you!!

yeah we were thinking, tokyo, osaka and kyoto. I just love it all, the culture/religion and morals but also the western aspects aswell. We have a rough idea but as it's our first time just thought we would see what people suggest :)

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If all you can say about your interests is that, it is very hard for people to give you any specifics on what to do and see. Contrary to what bamse wrote, I'd rather skip Tokyo or at least spend only a little time there.

Rather than ask whether you've looked at a guide book, how about this: what have you found in guide books that interests you so far?

You're not going to experience much in the way of morals as a tourist.

4

You should begin with buying a guide book.