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All major currencies, except the Japanese yen, are priced to four decimal places. In such case, a pip is one unit of the forth decimal point, or 1/100th of one percent.
For the Japanese yen, a pip refers to one unit in the second decimal point, for the reason that the yen is much closer in value to one hundredth of other major currencies.
by Ninja, askpips.com
In the case of the USD/JPY pair, only two decimal places are used because the JPY is so cheap compared to the dollar. One pip doesn't necessarily mean 0.0001 for all currency pairs... A pip is dependent on the currency pair we are talking about. Another example of a "cheap" currency pair is the USD/KRW (Korean Won).
by ForexNinja, askpips.com