Disclaimer: This theory was not thought of by me. I ran into it on another Naruto site and thought to show it here
I believe Naruto has a secret kekkei genkai ability that is unknown to most everyone in the series.
The first piece of evidence that supports my theory is a statement by Yamato. In chapter 299, entitled "The Source of Strength", Yamato makes the following observations about the Kyuubi's chakra:
"The Kyuubi's chakra is acting like poison..something like that can't simply be healed by Sakura's level of healing jutsu. Which makes me even more surprised that Naruto is able to endure it."
"Your true strength isn't from Kyuubi's power, and the reason you're able to stand Kyuubi's chakra is because of the strength of your own chakra."
The above quote implies that Naruto's own chakra holds some special properties that normal people's chakra lack. Naruto, on his own can withstand the negative effects of the Kyuubi's chakra. This is a fact supported by the manga itself.
There are currently only two known kekkei genkai abilities that can control the Kyuubi's chakra. The first is the Mangekyou Sharingan as noted here & here. While unconfirmed, it is believed that Mangekyou Sharingan controls the Kyuubi through the use of genjutsu. It is quite obvious that Naruto has neither Mangekyou Sharingan or genjutsu strong enough to control the Kyuubi. The only other known kekkei genkai that possesses the ability to control Kyuubi chakra is the unnamed kekkei genkai ability of Hashirama Senju, the first hokage. Yamato, a clone of Hashirama demonstrates this ability here & here. He then explains why only he can use the ability here & here.
It is my belief that the hidden kekkei genkai that Naruto possesses is the same one Hashirama Senju had. I also believe that Haku of the land of water also had this ability. The abilities of Haku & Hashirama were simply named after the elements they created by combining their elemental affinities. Hashirama's being Mokuton(earth+water) & Haku's being Hyouton(wind+water). I believe their abilities came from the same source. That source is the kekkei genkai(bloodline limit) of the Uzumaki clan.
Not much is known about the Uzumaki clan, however we do known Naruto's mother was from the Uzumaki clan, as well as the Whirlpool Country. It is possible that the former Whirlpool Country was the home of the Uzumaki clan, however something happened to the Whirlpool Country. Since it is refered to as the "former" Whirlpool Country, it is safe to assume something happened to the country to cause it to no longer exist.
The Whirlpool Country invaded by the bloody mist which was controlled by none other than Madara Uchiha(He controlled Yagura, the mizukage).
Kushina Uzumaki was from the ruling family of the Uzumaki clan, she was saved from certain death before the invasion & taken to Konoha to become kyuubi's new jinchuuriki with her distant cousins the Senjus. Hashirama has an Uzumaki wife. It is not far-fetched to say that the Senju and Uzumaki are related. After all, why would a senju member a non-senju. Uchiha only married Uchiha and it was the same way for other clans. The Uzumaki carry a certain kekkei genkai that we witnessed early in the manga. Did you ever notice anything interesting about the Senju?
Hashirama and Tobirama both have a water elemental affinity (I am not saying that his Kekke Genkai is the water affinity. I will elaborate later). This would also explain why Nidaime was so skilled with his water elemental jutsu. The affinity for water is most likely pasted down through the Uzumaki/Senju genes in a similiar manner to the fire elemental affinity of the Uchiha clan.
The Senju and Uchiha are opposited, after all. There is a possibility that Minato and Kushina were aware of Naruto's Kekkei Genkai and therefore concluded that Naruto could control the Kyubi one day.
There are two things that further reinforce my belief. Kishimoto often uses symbolism to hint at certain plot points. I believe the following instances of symbolism point to a connection betweeb Naruto & Hashirama Senju:
very first page of the manga
Naruto has just defaced the Hokage monument, he even signs his work. The funny thing about this is where Naruto signs his name. Naruto's name appears on Hashirama, the Shodaime Hokage & Minato Namikaze, the Yondaime Hokage. One of these men has already been revealed to be Naruto's father, could the other also have a blood relation to Naruto? Naruto signs the name Uzumaki with the same spiral he wears as a clan symbol. The spiral is the symbol of the Uzumaki clan.
Madara knew that Naruto's Kekkei Genai could pose a threat to him one day, after reviving the jyuubi. He saw it for himself during his battle with Hashirama Senju. Hashirama controlled the kyuubi and other bijuu. What could stop another kekke genkai from being able to manipulate the Juubi itself?
Then there is that defining moment at the Valley of the End, where Naruto stood on Hashirama's head & Sasuke on Madara's head, here.
Now, I also believe that Haku share the same blood as Naruto & Hashirama. I believe that the current Water Country was once the former Whirlpool Country. Madara Uchiha after his defeat at the hands of Hashirama, took the opportunity of his apparent death to leave the land of fire. Madara took his time with his plan. He told Sasuke that he needs to be patient so he could achieve his goals. Hell, Madara has all the time in the world.
Madara Uchiha went in search of the source of Hashirama's power & he found it. Madara Uchiha learned that Hashirama was a descended of the Uzumaki clan & that a select few of the Uzumaki clan had a special kekkei genkai. Madara wanted to destory the source of Hashirama Senju's power,
so he manipulated the mizukage, Yagura to start a genocide against Kekke Genkai holder including the Uzumaki clan, those in possession of the very same Kekke Genkai that led to his defeat at the Valley of the End. The genocide was opposed by many of course and became a civil war which led to the deaths of many Uzumaki clan members as well as other clans with kekkei genkai abilities from the Whirlpool Country. Madara's side won & the Hidden Mist was renamed the Bloody Mist Country.
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.
Kishimoto foreshadows the future of the plot in many ways. A common method, as you know, are the manga chapter covers. This cover interests me. If you look behind Naruto and Haku, there is the Uzumaki symbol on the top of the building. Why would Haku be next to an uzumaki symbol? You know my answer. They are related in being seen as tools and being uzumaki.
Kishi, also, foreshadowed what is to happen by adding the word "Shippuden" to the part 2 of the story. Why "Shippuden"? The word "Shippuden" means hurricane in japanese. And what are hurricanes made out of? Water and Wind.
Naruto's second elemental affinity will be water.
There was another character with that same Kekke Genkai... Done guessing? it was Mei Terumi. Mei is capable of using the earth, fire, and water natures, and has two kekkei genkai. She is able to combine water and fire to create vapor or mist. She isnt able, however, to create wood. That is because she did not grow in woodsy enviorments. It is my belief that she is related to the Uzumaki/Senju in some way
In conclusion, it is my belief that Naruto possesses the same kekkei genkai as Hashirama Senju & Haku of the Water Country. Naruto's second elemental affinity will be water & he will use his kekkei genkai to combine his wind & water elemental affinities to create a hurricane 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. Naruto may also discover a third elemental affinity for earth, allowing him to use Mokuton 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. The only thing keeping Naruto's kekkei genkai from manifesting is the Kyuubi. Now that he can control the Kyubi, he will soon find out about his Kekke Genkai.
Combining water and wind. Does that sound vaguely familiar to anyone?
So what is Naruto's Kekke Genkai?
The power to combine water affinity with others.
Thanks to everyone who took the time to read this wall of text.