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In Naruto, a number of "ninja clans" are referenced. Those include Uchiha and Hyuga. Those two both have kekkai genkais. It seems as though ninja clans are just families with kekkai genkais, but I'm wondering if that is every explained or specified anywhere. Also, what are the known ninja clans (if that won't be too long a list)?

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    A clan is a family which shares a common characteristic, not necessarily kekkei genkai. The Uzumaki clan was well known for their prowess in fuinjutsu and strong life force, which are not kekkei genkai. Hmm, well, maybe they are. – Masked Man Mar 8 '13 at 16:26
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The Naruto wiki page on clans has a good explanation of what a clan is, plus a list of all the known clans. To sum up, it goes something like this:

First, it is important to notice that the kanji used is 一族 (read Ichizoku), which literally means family. So, clans are families or groups of shinobi that constitute a basic unit of a village. The Senju and Uchiha clans were the first known clans to form an alliance to create a village, which was an example followed by many clans. As you referred, belonging to a clan is usually defined by genetics/blood, which is of the utmost importance in the usage of kekkei genkai. Also, clans pass down from generation to generation said kekkei genkai or other jutsu which are a specialty to the clan, which shinobi unaffiliated to any clan do not seem to do with their regular jutsu. Some clans are extensive and composed of several families, while others are just composed of a nuclear family.

List of known clans:
- Aburame clan - Konohagakure
- Akimichi clan - Konohagakure
- Amagiri clan - Yumegakure (Naruto Shippūden: Kizuna Drive game only)
- Fuuma clan - Amegakure
- Another Fuuma clan - Otogakure
- Hagoromo clan - No village (pre-village era)
- Hirasaka clan - Yumegakure (Naruto Shippūden: Kizuna Drive game only)
- Hōzuki clan - Kirigakure
- Hyūga clan - Konohagakure
- Inuzuka clan - Konohagakure
- Jūgo's clan - Unknown village/no affiliation (Jūgo is the only known member)
- Kaguya clan - Unknown village/no affiliation
- Kamizuru clan - Iwagakure (anime only)
- Kedōin clan - Unknown village/no affiliation (anime only)
- Kohaku clan - Had their own village in the Fire Country, associated with Konohagakure (anime only)
- Kubisaku clan - Unknown village, located in the Land of Neck (anime only)
- Kurama clan - Konohagakure (anime only)
- Nara clan - Konohagakure
- Rinha clan - Unknown village/no affiliation (Naruto Shippūden 3D: The New Era game only)
- Ryū clan - No village (pre-village era, Naruto Shippūden: Dragon Blade Chronicles game only)
- Sarutobi clan - Konohagakure
- Senju clan - Konohagakure
- Shiin clan - Otogakure (anime only)
- Shirogane clan - Sunagakure (Naruto: Uzumaki Chronicles 2 game only)
- Tenro clan - Yumegakure (Naruto Shippūden: Kizuna Drive game only)
- Tsuchigumo clan - Tsuchigumo Village (anime only)
- Uchiha clan - Konohagakure
- Uzumaki clan - Uzushiogakure
- Wagarashi family - Land of Tea (anime and Naruto: Path of the Ninja 2 game only)
- Wasabi family - Land of Tea (anime only)
- Watari ninja - Unknown village/no affiliation (anime only)
- Yamanaka clan - Konohagakure
- Yotsuki clan - Kumogakure
- Yuki clan - No village, Land of Water

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