Naruto does have a kekkei genkai, but it's not a doujutsu. Naruto has the same kekkei genkai as Haku & Hashirama Senju. Naruto Uzumaki, Haku & Hashirama have one thing in common, they're all descended from the Uzumaki clan through their mothers. What does this mean? Naruto will be able to combine two elemental chakras to create a new element. Just like Haku & Shodaime.
Let me explain, Hashirama Senju & Nidaime's mother was from the Uzumaki clan of the Whirlpool Country. They inherited their water elemental affinity from their mother. The Uzumaki clan inherits water elemental affinities just like the Uchiha clan inherits fire elemental affinities. This is also why Nidaime's water jutsu was so strong even without a source of water. Hashirama inherited his earth elemental chakra affinity from his father. Shodaime combined his earth elemental chakra & water elemental chakra with his kekkei genkai, creating Mokuton(the wood element).
After Madara Uchiha was defeated at the Valley of the End by Hashirama. He took the opportunity his apparent death gave him to leave the land of fire. Madara Uchiha was in search of the source of Hashirama power & he found it. Madara Uchiha learned that Hashirama was a descended of the Uzumaki clan & that the Uzumaki clan had a special kekkei genkai. Madara wanted to destory the source of Hashirama Senju's power, so he started a rebellion against the Uzumaki clan, rulers of the then Whirlpool Country. The civil war lead to the death of many Uzumaki clan members as well as other clans with kekkei genkai abilities from the Whirlpool Country. Madara's side won & the Whirlpool Country was renamed the Water Country. Madara became the Mizukage. Those with kekkei genkai abilities were persecuted, those who were still alive went into hiding.
Haku's mother was one of the Uzumaki clan members that survived, she fled to the snowy northern region of the now Water Country. Their she met a man & got married. She eventually gave birth to Haku, of course you know what happened next. Haku discovered the Uzumaki clan's kekkei genkai on his own. His father then killed his mother & Haku killed his father & the other villagers in self defense. Those with kekkei genkai abilities were considered the cause of the civil war, so they were always hunted & killed. Haku met Zabuza & they begin their journey together. Haku combined his water elemental chakra & wind elemental chakra to create Hyouton(the ice element). Haku used his elemental affinities to create Hyouton because he was born in a snowy region of the Water Country & it was natural for him to create ice.
Kushina Uzumaki was the rightful heir of the Whirlpool Country(now the Water Country). During the time of the civil war, Kushina Uzumaki was saved & sent to Konoha to live with her cousins Hashirama & Nidaime. There she grew up & met Minato Namikaze the future 4th Hokage. They fell in love & had a child together. That child is Uzumaki Naruto. The women of the Uzumaki clan carry the necessary genes needed to pass down the kekkei genkai of the Uzumaki clan. Those born with only one parent of Uzumaki descent have a very slim chance of gaining the clans kekkei genkai. This is why Hashirama was the only one to gain the kekkei genkai. There was probably only a 50/50 chance that he would gain the ability. Nidaime never did. Hashirama was unable to pass down the kekkei genkai because he was not female, so no one else in his bloodline gained the ability.
This kekkei genkai of the Uzumaki clan exist currently in Naruto Uzumaki. It's what keeps the Kyuubi's chakra from killing him. Yamato said himself that the Kyuubi's chakra is like a poison:
http://read.mangashare.com/Naruto/ch...9/page004.html
The Uzumaki's clan other ability, the ability to control bijuu, allows Naruto to survive the Kyuubi's poisonous chakra. Naruto won't fully awaken to his kekkei genkai until much later in the series. He'll combine his wind & future water elemental chakra into a rain/storm element. Since Naruto is from a warmer climate this will be more natural for him, but he might also be able to create Hyouton. Naruto will be able to control the rain itself. He will also be able to create whirlpools & tidalwaves as well. Another thing is since Naruto possesses Shodaime's chakra crystal necklace, he will receive the same benefit that Shodaime did. Naruto will be able to bend Bijuu's & their chakra to his will.
I have some serious evidence to back this theory up, but I won't post all of it. I will however, provide you with a view things that show the links between Naruto, Hashirama Senju & Haku.
In the very first chapter of the series Naruto writes his name "Uzumaki" on the faces of the Hokages. The spiral is the symbol of the Uzumaki clan & it's how Naruto writes his family name. A name that was given to him because he was the last of an important & powerful clan & it's rightful heir. The most important thing about that part in the first chapter is the Hokage faces that he writes his name on:
http://read.mangashare.com/Naruto/ch...1/page004.html
The spiral, symbol of Naruto's clan name is on the faces of the First & Fourth Hokages. One of these men just so happens to be his father. We'll just have to wait & see about Shodaime.
BTW, heres proof that Naruto signs his name with spirals:
http://read.mangashare.com/Naruto/ch...9/page004.html
Naruto signs his name on the toad contract with a spiral.
Another thing is the fact that Konoha ninja wear spiral patches on their uniforms. One on each shoulder & one on the back. The spiral is the opposite direction of Naruto's, but they represent the same thing. Hashirama had the symbol placed on the Hidden Leaf's uniform because the Uzumaki clan was the source of his power. In fact the Konoha leaf symbol is a combination of a leaf & the Uzumaki clan's spiral symbol. The best example of this is found during the chapter Naruto is learning the second step for Rasengan:
Jiraiya had drawn the spiral in the palm of Naruto's hand to get him to focus:
http://read.mangashare.com/Naruto/ch...4/page010.html
After a flashback Naruto changes the spiral into the leaf symbol to better focus himself:
http://read.mangashare.com/Naruto/ch...4/page011.html
This is what Naruto envisions when he focuses:
http://read.mangashare.com/Naruto/ch...4/page012.html
I believe Minato was inspired to come up with Rasengan because of the Uzumaki clan symbol. His wife was from that clan after all.
This chapter cover shows Sakura, Naruto & Sasuke with their respective clan symbols above their heads:
http://read.mangashare.com/Naruto/ch...7/page002.html
Funny thing is, this chapter cover is one of the covers that appear if you apply Jiraiya's code to the chapter covers
9, 31, 8, 106, 7, 207, 15
In fact, if you add up those numbers you get 383, the number of the chapter that the code first appears in. This is actually apart of another theory of mine that I've posted on another forum. I would suggest that you take the time to look at those chapter covers, just make sure you find the "actual" numbered chapter covers & you follow the order of the code. Those who can see underneath the underneath may be able to find the hidden meaning.
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