Realizing both had their own style regarding the designs, Kishimoto decided to draw manga while crafting his own images. This made him analyze the artwork of Akira 's original author, Katsuhiro Otomo, as well as Akira Toriyama, another artist he admired. While as a child, Kishimoto enjoyed reading manga, he was inspired to write one after seeing a promotional image for the film Akira. In 2010, Kishimoto also produced a one-shot baseball manga, Bench ( ベンチ, Benchi ?), as part of Jump's 'Top of the Super Legend' project, a series of six one-shot manga by famed Weekly Shōnen Jump artists, also including Sorachi Hideaki, Konomi Takeshi, Usuta Kyosuke, Akimoto Osamu, and Akira Toriyama.

In 2009, Kishimoto designed an extra costume for the video game character Lars Alexandersson for Tekken 6, and in 2010 this character appeared in Naruto Shippuden: Ultimate Ninja Storm 2 as part of a special cross-promotion. The seventh volume of Viz's release became the first manga to ever win a Quill Award when it claimed the award for 'Best Graphic Novel' in 2006. The Naruto manga series has become one of Viz Media's top properties, accounting for nearly 10% of all manga sales in 2006. Naruto is still ongoing, with more than 52 volumes and just over 50 released in English, and has sold over 100 million copies in Japan and over 95 million copies were sold in the US followed by over 93 million copies worldwide (outside Japan and United States) as of volume 36, also being adapted into two successful anime series. In 1999, a serialized version of Naruto began publication in Weekly Shōnen Jump and quickly became a hit. In 1998, Kishimoto premiered as a Weekly Shōnen Jump artist with a serialized version of Karakuri in Weekly Shōnen Jump, but it proved unpopular and was canceled soon after. This was followed in 1997 by a pilot version of Naruto ( NARUTO－ナルト－ ?), published in Akamaru Jump Summer. This earned him the Weekly Shōnen Jump's monthly 'Hop Step Award' in 1996, granted to promising new manga artists. Kishimoto's first work as a manga artist was Karakuri ( カラクリ ?), which he submitted to Shueisha in 1995.

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