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On line reservation : JR East Area

 
Take the train in Japan

shinkansen and limiteD express

This is the only website with a reservation online system. Once you have ordered a Japan Rail Pass, you can visit the JR East website, registered and get some reservations for the train you selected. Reservations will be available in the ticket office of the station of your choice in the JR east area (Tokyo metropolitan area, Kanto, Tohoku, Joshinetsu) and JR Hokkaido areas.

 
On line reservation for the Hokkaido shinkansen with a Japan Rail Pass
JR EAST and JR Hokkaido TRAIN RESERVATIONIt is available one month before your journey. The reservation must collected the day before the departure date. If you do not collected the tickets by then, a 310 yen cancellation fee will be charged. You can change the reservation once.

It does not concern Tokaido shinkansen, Sanyo shinkansen and Kyushu shinkansen.
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The Hokuriku shinkansen with a Japan Rail Pass
It concerns the shinkansen : 
- The Hokkaido Shinkansen : the Hayabusa and Hayate,
- The Tohoku Shinkansen : the Hayabusa, Hayate, Yamabiko and Nasuno,
- The Akita Shinkansen : the Komachi,
 -The Yamagata Shinkansen: the Tsubasa and Toreiyu Tsubasa,
- The Joetsu Shinkansen: the Max Toki, Toki, GENBI SHINKANSEN Toki, Max Tanigawa and Tanigawa, 
- The Hokuriku Shinkansen : the Kagayaki, Hakutaka, and Asama

It concerns also some JR East Limited Express on the following lines : 

- The Narita Express between the Tokyo metropolitan area and Narita International Airport
- The Joban Line: the HITACHI and TOKIWA between the Tokyo metropolitan and Mito/Iwaki areas,
- The Chuo Line: the Super Azusa, Azusa and Kaiji between the Tokyo metropolitan and Kofu/Matsumoto areas,
- The Tokaido/Ito and the Izu Kyuko Lines: the Super View Odoriko and Odoriko between the Tokyo metropolitan and Izu areas, 
- The Tobu Railway Line: the Nikko, SPACIA Nikko, Kinugawa and SPACIA Kinugawa between the Tokyo metropolitan and Nikko/Kinugawa 
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The Super Hokuto Limited Express with a Japan Rail Pass
And some  JR Hokkaido Lines Limited express trains and rapid trains on the following lines :

- The Hakodate Line: the Super Hokuto and Hokuto: between the Sapporo metropolitan area and Hakodate,
- The Muroran Line: the Suzuran between Sapporo and Higashi-Muroran,
- The Chitose/Hakodate Line: the Rapid Airport between Otaru and New Chitose Airport,
- The Sekihoku Line: the Okhotsk between the Sapporo metropolitan area and Abashiri, and the Taisetsu between Asahikawa and Abashiri,
- The Soya Line: the Sarobetsu between Asahikawa and Wakkanai, and the Kamui and Lilac between Sapporo and Asahikawa, 
- The Sekisho/Nemuro Line: the Super Tokachi between the Sapporo metropolitan area and Obihiro, and the Super Ozora between the Sapporo metropolitan area and Kushiro
 
Online seat reservation are also  available for some Joyful trainsHIGH RAIL 1375, IZU CRAILE, Kirakira Uetsu, Koshino Shu*Kura (Yuzawa Shu*Kura, Ryuto Shu*Kura), Oykot, POKÉMON with YOU Train, Resort Asunaro (Shimokita), Resort Minori, Resort Shirakami ,Resort Umineko, Resort View Furusato, SL Banetsu Monogatari, SL Ginga, SL Gumma Minakami,  SL Gumma Yokokawa, Zipangu (Hiraizumi).

You can find more detailed information on JR East Website. 
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