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TheLegendaryWolf on 29 June 2015
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"Nintendo published an updated listing of its subsidiaries and affiliated companies as part of a new securities report. There are 27 consolidated subsidiaries (down slightly from last year’s count of 29) and six affiliated companies."

First, some notes:

– SiRAS.com Inc is no longer a subsidiary
– Capital of Nintendo RU LLC. increased from RUB104 to RUB336
– Nintendo European Research and Development SAS is now a wholly owned subsidiary
– Nintendo’s ownership of Nd Cube Company, Ltd. increased from 96% to 97%
– Another subsidiary/affiliated company no longer with Nintendo is Silicon Knights

"All of Nintendo’s subsidiaries and affiliated companies are listed below."

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Subsidiaries

Name: Nintendo of America Inc
Region: United States of America
Capital (in thousands): $110,000
Corporate role: Sales/marketing
Ownership percentage: 100

Name: Nintendo of Canada Ltd.
Region: Canada
Capital (in thousands): $110,000
Corporate role: Sales/marketing
Ownership percentage: 100

Name: Nintendo of Europe GmbH
Region: Germany
Capital (in thousands): €30,000
Corporate role: Sales/marketing
Ownership percentage: 100

Name: Nintendo France S.A.R.L.
Region: France
Capital (in thousands): €10,000
Corporate role: Sales/marketing
Ownership percentage: 100

Name: Nintendo Benelux B.V
Region: Netherlands
Capital (in thousands): €6,800
Corporate role: Sales/marketing
Ownership percentage: 100

Name: Nintendo Iberica, S.A.
Region: Spain
Capital (in thousands): €3,000
Corporate role: Sales/marketing
Ownership percentage: 100

Name: Nintendo RU LLC.
Region: Russia
Capital (in millions): RUB336 (was RUB104 in 2014)
Corporate role: Sales/marketing
Ownership percentage: 100

Name: Nintendo Australia Pty. Ltd.
Region: Australia
Capital (in thousands): AUD8,500
Corporate role: Sales/marketing
Ownership percentage: 100

Name: Nintendo Taiwan Co. Ltd.
Region: Taiwan
Capital (in thousands): NT$5,000
Corporate role: Sales/marketing
Ownership percentage: 100

Name: Nintendo of Korea Co. Ltd.
Region: South Korea
Capital (in thousands): ₩25,000
Corporate role: Sales/marketing
Ownership percentage: 100

Name: iQue, Ltd
Region: China
Capital (in thousands): $28,000
Corporate role: Sales/marketing
Ownership percentage: 100

Name: Nintendo Technology Development Inc.
Region: United States of America
Capital: The list states 1 US$, I assume they mean a million US$
Corporate role: Development
Ownership percentage: 100

Name: Nintendo Software Technology Corporation
Region: United States of America
Capital (in thousands): $20
Corporate role: Development
Ownership percentage: 100

Name: Retro Studios, Inc.
Region: United States of America
Capital (in thousands): $10,001
Corporate role: Development
Ownership percentage: 100

Name: Nintendo (Hong Kong) Co., Ltd.
Region: Hong Kong
Capital (in thousands): HK$49,300
Corporate role: Sale/marketing
Ownership percentage: 100

Name: Nintendo European Research and Development SAS
Region: France
Capital (in thousands): €300
Corporate role: Development
Ownership percentage: 100 (was 97% in 2014)

Name: Nd Cube Company, Ltd.
Region: Japan (Tokyo)
Capital: ¥483000000
Corporate role: Development
Ownership percentage: 97 (was 96 % in 2014)

Name: 1-UP Studio Co., Ltd.
Region: Japan (Tokyo)
Capital (in millions): ¥90
Corporate role: Development
Ownership percentage: 100

Name: Monolith Software, Ltd. (was Inc.)
Region: Japan (Tokyo)
Capital (in millions): ¥75
Corporate role: Development
Ownership percentage: 97

Name: Nintendo Network Service Database Inc.
Region: Japan (Tokyo)
Capital (in millions): ¥480
Corporate role: Other (network services)
Ownership percentage: 100

Name: Mario Club Co., Ltd.
Region: Kyoto
Capital (in millions): ¥450
Corporate role: Development (debugging)
Ownership percentage: 100
In addition to the above, there are five consolidated subsidiaries.

Affiliated companies

Name: Pokemon Co., Ltd.
Region: Tokyo
Capital (in millions): ¥365
Corporate role: Sales of Pokémon
Ownership percentage: 32

Name: Warp Star Co., Ltd.
Region: Tokyo
Capital (in millions): ¥10
Corporate role: Animation, IP/rights management
Ownership percentage: 50

Name: PUX Co., Ltd.
Region: Osaka
Capital (in millions): ¥45
Corporate role: Development of audio and video processing software
Ownership percentage: 27

Source:http://nintendoeverything.com/latest-listing-of-nintendo-subsidiaries-and-affiliated-companies/#more-208033 and http://www.neogaf.com/forum/showthread.php?t=1072343