According to the Dengeki G's Magazine 2008 May issue, Kyoto animation will make the second season of CLANNAD titled "CLANNAD AFTER STORY". The voice actors and the production staffs are the same as the first season. Director Ishihara wondered whether they should finish the CLANNAD anime at the end of Nagisa's main arc or continue to the after story, but they decided to make the second season after long discussions.

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There are so many unreliable information about when it will start and how long it is. Seems like it will start this summer and it's 12-13 episodes.
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Additional Info from Tokyo International Anime Fair
8th vol of CLANNAD DVD includes "Tomoyo another story" (not "Tomoyo after"), kind of supplement of Tomoyo's arc.
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Edited===========
CLANNAD AFTER STORY due this fall
Scan of AniMedia Aug issue