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Pending an update where I will organize all the jutsu in there own alphabetical sections, which will make it easier to find the jutsu you are looking for. Keep up the good work and suggest more jutsus so I can find there weaknesses. 
I have added scans featuring said jutsu's along with the explanation of there weaknesses for people to better understand them. Feel free to state your own jutsu you would like to see a weakness for to help build.
Itachi once proclaimed that every jutsu has a weakness. But even with his feats people find it hard to believe that every jutsu really does have a weakness. And so I have created this thread, I shall put his claim to the test.
So if you have any jutsu that you question whether or not it has a weakness feel free to let me know and I will add it to my thread giving you a plausible weakness within the jutsu.
Tailed Beast Bomb
Great Shark Bullet
FTG aka Hiarishin
Lightning Release: False Darkness
Kamui
Tsukuyomi, KA, or Any Genjutsu (Including Frill Necked Lizard)
Edo Tensie
Rasengan (All Variations)
Sage Art: Inorganic Reincarnation
Summoning Jutsu
I have added scans featuring said jutsu's along with the explanation of there weaknesses for people to better understand them. Feel free to state your own jutsu you would like to see a weakness for to help build.
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Itachi once proclaimed that every jutsu has a weakness. But even with his feats people find it hard to believe that every jutsu really does have a weakness. And so I have created this thread, I shall put his claim to the test.
So if you have any jutsu that you question whether or not it has a weakness feel free to let me know and I will add it to my thread giving you a plausible weakness within the jutsu.
Let see if every jutsu really does have a weakness 
How this works
How this works
Its simple, I am building a list of all the jutsus you guys can think of and then listing out weaknesses within the jutsu. Now these weaknesses may not completely counter the jutsu but will more than likely be flaws within the jutsu that once exploited make it alot more manageble and easier to counter.
Ill be checking up on the thread frequently, simple post the name of the jutsu. I will look it up and find a plausible weakness within it. The tougher/stronger the jutsu the better, if you give me a good one I will give you rep and if you stump me I will place your jutsu at the top so everyone knows who found the 1 jutsu that disproves itachis claim.
After looking up your jutsu I will send you a message letting you know your jutsu has been added and that a weakness has been found.
Ill be checking up on the thread frequently, simple post the name of the jutsu. I will look it up and find a plausible weakness within it. The tougher/stronger the jutsu the better, if you give me a good one I will give you rep and if you stump me I will place your jutsu at the top so everyone knows who found the 1 jutsu that disproves itachis claim.
After looking up your jutsu I will send you a message letting you know your jutsu has been added and that a weakness has been found.
Jutsu so far:
Tailed Beast Bomb
The weakness of the tailed beast bomb is the fact that the bijuu must gather the chakra for it outside there body. To use it they spend about 3-5 seconds, the time increases based on how much more chakra they want to put into it, afterwards they consume the chakra and then let it out in the form of the blast. So fired a blast into the ball of chakra prior to the bijuu eating it then it would take the brunt of the damage to itself.
Think of it like this, the tailed beast bomb is a water balloon. The tailed beast must fill it up with water, then eat it in order to direct the blast, then throw it at you. But if you popped the balloon before the bijuu got the chance to eat it, it would explode in its face drenching him in water.
Think of it like this, the tailed beast bomb is a water balloon. The tailed beast must fill it up with water, then eat it in order to direct the blast, then throw it at you. But if you popped the balloon before the bijuu got the chance to eat it, it would explode in its face drenching him in water.
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Great Shark Bullet
The fact that it is so big it reduces the users field of vision, so if you were to somehow dodge it or survive the blast he would have a very hard time finding out if he really did hit you. Which could open up a chance to counter attack. This is a problem with alot of large scale jutsu as if they do hit they will destroy every evidence of you, so there is no way of knowing whether it hit you and left no trace of you or if it just missed.
*Granted Kisame's body did survive the explosion but that was only because the brunt of it was absorbed by his jutsu, had he of taken the full force of Hidorama he would have been blown to bits, the same goes for his Great Shark Bullet which is arguably stronger.*
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*Granted Kisame's body did survive the explosion but that was only because the brunt of it was absorbed by his jutsu, had he of taken the full force of Hidorama he would have been blown to bits, the same goes for his Great Shark Bullet which is arguably stronger.*
FTG aka Hiarishin
Before the 4th Raikage was even officially the Raikage he displayed a way of countering this technique. It is quite simple, the seals themselves give it away.
If you account for all the seals of the battle field you can effectively figure out where the 4th will strike from. Which negate its element of surprise. But also can give you the advantage as Minato is temporarily blind while teleporting, if within this brief instance you can launch your own attack you can catch him off guard, assuming you have determined which seal he will teleport to.
Although Raikage had the right Idea it was actually Killer Bee who put this in action, knowing that Minato would teleport behind him and thus giving him an opportunity to take him out.
*Before we get to it though I would like to point out that the seal can be removed by destroying whatever the seal was placed on, be it a boulder, a shirt, or a kunia.*
If you account for all the seals of the battle field you can effectively figure out where the 4th will strike from. Which negate its element of surprise. But also can give you the advantage as Minato is temporarily blind while teleporting, if within this brief instance you can launch your own attack you can catch him off guard, assuming you have determined which seal he will teleport to.
Although Raikage had the right Idea it was actually Killer Bee who put this in action, knowing that Minato would teleport behind him and thus giving him an opportunity to take him out.
*Before we get to it though I would like to point out that the seal can be removed by destroying whatever the seal was placed on, be it a boulder, a shirt, or a kunia.*
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Lightning Release: False Darkness
Although it is pressumed to be fast it really isnt given the fact that Shikamaru, a person with no feats revolving speed, was able to dodge it given very little prep.
It is hard to talk about this jutsu since it isnt really cannon but is only seen in the anime. And I dont really want to discuss non cannon jutsu here.
On top of that keep in mind that all the creatures created by kakuza's abilities have a breif charge up period, kin to forming seals. This is a dead give away.
It is hard to talk about this jutsu since it isnt really cannon but is only seen in the anime. And I dont really want to discuss non cannon jutsu here.
On top of that keep in mind that all the creatures created by kakuza's abilities have a breif charge up period, kin to forming seals. This is a dead give away.
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Kamui
Like alot of MS abilities the jutsu itself is its biggest weakness. It places huge amounts of stress on the user thus limiting the jutsus usage to maybe 3 to 4 times before completely draining the user. And with that same logic you can deduce that MS abilities biggest weakness lies in the fact that they can be dodged. Kamui is especially easy to be dodged as it is fairly easy for any low level sensor to notice the MS user pooling together a large amount of chakra.
Long Distance Kamui
Short Range Kamui
Intangibility
Long Distance Kamui
After using the jutsu to attempt to kill diedara Kakashi states that he missed and this was because Deidara noticed it in time and was able to dodge it, but his arm was collateral damage. Below this we see him gathering up chakra to attempt another kamui, but Deidara is on to what he is doing and dodges it before he can get him.
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Short Range Kamui
There biggest weakness of the short range Kamui is displayed by Minato when he fights against the Masked Man. For the Short Ranged Kamui to be used the user must not only come into physical contact with his opponent but he must also make himself physical. Minato exploits this quite easily.
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Intangibility
Well its hard to say it because the only weaknesses we have seen is another kamui. But the fact that the intangibility is a double edged sword can also be considered a weakness. Yes you cannot tough him but he also cannot touch you. And so the only way for the battle to ensue he must become tangible eventually.
Genjutsu should easily work through this though because genjutsu is usually used covertly, as in without the enemy knowing. And he cant dodge an attack that he doesnt see coming.
But if anything the most crucial weakness to the Intangibility is here, now although it will take some Intel to figure this out if anyone did i would put Obito at a huge disadvantage.
Also seeing as to how Obito has Senju DNA one can assume that a regular Uchiha would only be able to maintain this for perhaps 1 minute if not less.
Genjutsu should easily work through this though because genjutsu is usually used covertly, as in without the enemy knowing. And he cant dodge an attack that he doesnt see coming.
But if anything the most crucial weakness to the Intangibility is here, now although it will take some Intel to figure this out if anyone did i would put Obito at a huge disadvantage.
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Also seeing as to how Obito has Senju DNA one can assume that a regular Uchiha would only be able to maintain this for perhaps 1 minute if not less.
Tsukuyomi, KA, or Any Genjutsu (Including Frill Necked Lizard)
There are a few ways to counter Genjutsu. The first is that they cannot actually kill people, it can only get the brain to feel like the body is going through alot of pain. And thus if the person you are using it against has a strong mind they can endure the genjutsu. Now in a 1v1 this isnt much of a problem because you can just kill them while they are in the genjutsu, but when your with a team it becomes alot harder to do so.
The second method of combating Genjutsu is with Genjutsu Dissapation which is a method of disrupting the enemies chakra found within the victims body. Ofcourse this means you will have to have someone around you capable of doing so, this is displayed in the following scans.
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There is also a 3rd way of beating genjutsu which is to train yourself to act against it. Deidara managed to do this after meeting Itachi just once. Which either makes him a genius or shows that it isnt too tough to do.
Another way to stop genjutsu is to stop your chakra flow, which is a difficult thing to do. But is possible based on what Jiraiya says.
Lastly Granny Chiyo gives us some insightfull ways of fighting against a Sharingans Genjutsu. Along with kakashi backing up my assertion that using MS abilities weakens Uchiha.
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The second method of combating Genjutsu is with Genjutsu Dissapation which is a method of disrupting the enemies chakra found within the victims body. Ofcourse this means you will have to have someone around you capable of doing so, this is displayed in the following scans.
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There is also a 3rd way of beating genjutsu which is to train yourself to act against it. Deidara managed to do this after meeting Itachi just once. Which either makes him a genius or shows that it isnt too tough to do.
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Another way to stop genjutsu is to stop your chakra flow, which is a difficult thing to do. But is possible based on what Jiraiya says.
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Lastly Granny Chiyo gives us some insightfull ways of fighting against a Sharingans Genjutsu. Along with kakashi backing up my assertion that using MS abilities weakens Uchiha.
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Edo Tensie
Edo Tensie is the jutsu that allows one to bring dead ninja back from the dead. Now alot of people dont pay close attention to why kabuto does the things he does and thus miss out on a supposed weakness. He says that he allowed the Edo's to keep there personallity because of the psychological damage they inflict but considering how much help the Edos provide in defeating themselves and how Kabuto only takes control when he has no choice I think that the psychological damage was jjust a happy coincedence. As Obito already stated he was surprised that Kabuto was able to handle so many Edos at one time.
Allowing them to keep there personalities is in a sense is a cruise control where the Edo's hold a small portion of control but are forced to follow the command tags inside of then with ninja of strong will being able to break free. If that is the case Kabuto must then take manual control and focus on controlling said ninja.
So then we see the Edo User 2 options: He can either allow the Edos to keep there personallities and with that have them help the other ninja defeat them by either pointing out what the Edu user is doing or letting them know what they are doing and what there weaknesses are. This is rather plausible as mostly everyone revived has shown that they dislike being revived and controlled like puppets and would more than likely be willing to help anyone destroy the one who summoned them. Although it has been shown throughout the manga here are some scans of an Edo helping out the person they are being forced to fight.
Or his second option is to control the Edo's Manually which isnt an issue if you limit yourself to 2-3 powerful ninja like Orochimaru did. But you wont be able to summon an army like Kabuto did, else you run the risk of losing control.
Allowing them to keep there personalities is in a sense is a cruise control where the Edo's hold a small portion of control but are forced to follow the command tags inside of then with ninja of strong will being able to break free. If that is the case Kabuto must then take manual control and focus on controlling said ninja.
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So then we see the Edo User 2 options: He can either allow the Edos to keep there personallities and with that have them help the other ninja defeat them by either pointing out what the Edu user is doing or letting them know what they are doing and what there weaknesses are. This is rather plausible as mostly everyone revived has shown that they dislike being revived and controlled like puppets and would more than likely be willing to help anyone destroy the one who summoned them. Although it has been shown throughout the manga here are some scans of an Edo helping out the person they are being forced to fight.
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Or his second option is to control the Edo's Manually which isnt an issue if you limit yourself to 2-3 powerful ninja like Orochimaru did. But you wont be able to summon an army like Kabuto did, else you run the risk of losing control.
Rasengan (All Variations)
1) The Rasengan itself is a dense sphere of Chakra that is used like a sword, but Naruto and most Rasengan users dont always walk around with this sword like most real swordsman do. So it is hard to move around with it at high speeds and as you may notice many times when Naruto misses with his Rasengan he will often trip or stumble.
The fact that it is hard to manuevar with the Rasengan makes it incredibly linear and easily avoidable not to mention that once dodging it you can launch a counter attack.
2) The Rasengan is a pure chakra rotated in one direction creating a sphere. Much like someone swirling water in order to create a whirlpool. So one with understanding of the Rasengan and some training could possibly undo the rotation at the point of contact thus nullifying the Rasengan. The equivalent of swirling the water in the other direction. The only difference would be that because the action takes up little chakra but just requires chakra control you waste no chakra in undoing the Rasengan.
3) Again this comes back to the linear attack style of the Rasengan... It is like shooting a cannon ball at someone which you are attached to. It is strong but easy to counter as your wide open while charging, Naruto knows this and often employs clones and misdirection when using Rasengan to make it less obvious... But the average ninja is not as over powered as him *cough cough* i mean as well trained...
The fact that it is hard to manuevar with the Rasengan makes it incredibly linear and easily avoidable not to mention that once dodging it you can launch a counter attack.
2) The Rasengan is a pure chakra rotated in one direction creating a sphere. Much like someone swirling water in order to create a whirlpool. So one with understanding of the Rasengan and some training could possibly undo the rotation at the point of contact thus nullifying the Rasengan. The equivalent of swirling the water in the other direction. The only difference would be that because the action takes up little chakra but just requires chakra control you waste no chakra in undoing the Rasengan.
3) Again this comes back to the linear attack style of the Rasengan... It is like shooting a cannon ball at someone which you are attached to. It is strong but easy to counter as your wide open while charging, Naruto knows this and often employs clones and misdirection when using Rasengan to make it less obvious... But the average ninja is not as over powered as him *cough cough* i mean as well trained...
Sage Art: Inorganic Reincarnation
This is the technique that allows a Sage to manipulate the nature chakra running through the environment causing them to move according to his will. The jutsu is relatively quick although and is extremely deadly in closed off areas. But the jutsu loses its strength drastically in open areas where the only thing to manipulate is the ground. Even so it would make a good defensive jutsu.
Even so its main weakness is intense heat, In this instance we see the heat from the Amaterasu causing the Inorganic Reincarnation jutsu to become undone.
Even so its main weakness is intense heat, In this instance we see the heat from the Amaterasu causing the Inorganic Reincarnation jutsu to become undone.
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Summoning Jutsu
This sort of ties into the Greak Shark Bullet counter. Summons, especially the huge ones, can be impossible to handle at times. Even Orochimaru, the guy who took on Tsunade and Jiraiya, left the battle as soon as Manda was defeated because he knew there was no beating them.
Giant Summons
Small Summons
Giant Summons
And with that the biggest weakness of the Giant Summons are the fact that they are incredibly slow as well. The bigger they are the slower they are, except maybe Manda who has shown impressive agility, but not only that, with there huge size you look like a mere insect to them. Which means it is going to be hard to find you if you hide.
The weakness of a Summon is that it opens a chance to escape. Since the safest place to be is on the summons head or somewhere around it, one can easily use a offensive jutsu as a distraction to open a chance to escape.
Another weakness envolves the terrain, Giant Summons have a habit of destroying the place they are around during the battle. So if you engage your opponent somewhere that they dont want to see destroyed then you can effectively keep them from using Giant Summons.
The weakness of a Summon is that it opens a chance to escape. Since the safest place to be is on the summons head or somewhere around it, one can easily use a offensive jutsu as a distraction to open a chance to escape.
Another weakness envolves the terrain, Giant Summons have a habit of destroying the place they are around during the battle. So if you engage your opponent somewhere that they dont want to see destroyed then you can effectively keep them from using Giant Summons.
Small Summons
With these you trade off immense power for mobility and control. But smaller summons aren't often strong and at best could be treated as a 2nd ninja you have to fight during the battle. And giving one fatal blow they disappear into a cloud of smoke.
Just as the best way to counter an offensive jutsu is with a defensive jutsu, the best way to counter these summons is with summons of your own.
Just as the best way to counter an offensive jutsu is with a defensive jutsu, the best way to counter these summons is with summons of your own.
Enjoy 
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