The Japanese currency is the yen (in Japanese, en). There are two symbols for the yen: ¥ and 円.
The banknotes are:
New versions of the 1000 yen, 5000 yen, and 10,000 yen banknotes were issued in 2004, but the old ones are still valid.
In Japan, most transactions are done in cash, or by electronic money transfer (furikomi), which can be done from most ATMs and via your bank's online banking system. Checks (cheques) are not used, except by companies. Credit cards are accepted in many large stores, but in some areas it is still very common to find businesses (including hotels, restaurants etc.) that only accept cash.