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In Harry Potter and the Deathly Hallows, Nagini seemed to be able to see Harry and Hermione though Harry's invisibility cloak while they were visiting Harry's old house in Godric's Hollow.

Harry had the strangest feeling that she knew that they were there, and also who they were. Just as he reached this uneasy conclusion, she raised a gloved hand and beckoned.
- Harry Potter and the Deathly Hallows

Could the snake actually see them, or was it all based off of the assumption that someone was in front of the Potter's house and that it could be Harry?

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9  
Also, the Horcrux – Au101 Jan 27 at 16:49
36  
Why would you think Nagini "saw" them? Snakes have an excellent sense of smell. – Gorchestopher H Jan 27 at 16:49
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The Horcrux comment is a good point. The book does describe the locket as reacting to Nagini's presence. So maybe it works the other way around as well. – Joe JMC IT Jan 27 at 16:56
    
May be related: scifi.stackexchange.com/questions/7467/… – Xantec Jan 27 at 18:21
    
@GorchestopherH I'm pretty sure it never mentioned this, but for some reason I always interpreted it such that, since Harry's invisibility cloak was Death's, which made the wearer truly invisible, it also masked sounds and smells. Thinking about it though, I guess it probably wouldn't mask voices or smells. – TylerH Jan 28 at 14:47
up vote 35 down vote accepted

TL:DR - last line.

Adding on, I'd like to add this (under Behind the Scenes). It may be unreliable, but let me elaborate.

Many things could detect the Cloak, as we see in the series, such as the eye that Moody possesses, and the Marauder's Map. Now, the last bit sounds interesting.

It was also unable to hide Harry from creatures able to sense location by methods other than primarily sight, such as Dementors and Nagini.

Animals that use senses to roam could be able to see under the Cloak (possibly echo location, and snakes).

Dementors can as well, which may lead to snakes being able to.

"Dementors can’t see, you know. . . .” He swallowed. “They feel their way toward people by feeding off their emotions" - Sirius

Emotions such as fear can be sensed by Dementors - if you possess fear, they may be able to know where you are due to this, Cloak or not. As it only protects the user from some spells and sight, I'd assume the latter is correct.

Although different, Mrs. Norris, and Crookshanks may have sensed the presence of the Cloak as well.

As Dementors can sense Cloaks via a way of sensing fear, it reinforces the statement that snakes can sense the Cloak via smell, and possibly heat.

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7  
Interesting.. I'm surprised a "make-me-able-to-smell-things-incredibly-well" spell was never used in the (many) instances where people suspected nearby invisible persons, or even to track people (visible or not) like a hound might. – DoubleDouble Jan 27 at 18:06
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What do you mean by "detect the Cloak" or "sense Cloaks"? This makes no sense. Now, being able to detect what's inside of the cloak, despite the cloak's abilities makes perfect sense. – Ellesedil Jan 27 at 18:09
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@JanusBahsJacquet The cloak itself is protected against the summoning charm (one of the Death Eaters tries to "Accio Cloak" when they go to Hogsmede in Deathly Hallows but it doesn't work). I don't know if there's any mention of the cloak protecting the user from spells though. – Crow T Robot Jan 27 at 18:21
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@Ellesedil By "sense the cloak" I merely mean it and anything under it. – Jake Jan 27 at 18:24
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Snakes also have a keen sense of vibrations, and may have sensed Harry that way. – Kai Jan 28 at 1:16

Snakes don't see very well, they sense (and hunt and navigate) almost entirely through heat and smell.

According to Harry Potter wikia

http://harrypotter.wikia.com/wiki/Nagini

Nagini is most likely a fictional venomous Python. Pythons have heat receptors like pit vipers do.

Rowling has at least partially confirmed this theory:

Jess: How did nagini could see harry and hermione if they were under the invisibility cloak?

J.K. Rowling: Snakes’ sense are very different from human ones. They can detect heat and movement in a way that we can’t.

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i think your correct and your statements a good answer, however, I'd perhaps link to something confirming this ability of snakes to verify. – Himarm Jan 27 at 16:49
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Cobras don't have pits to sense heat. – Axelrod Jan 27 at 16:59
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@DoubleDouble And Nagini isn't a viper. She has a hood. – Axelrod Jan 27 at 18:14
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@DoubleDouble And the king cobra grows to 18 feet, not rarely up to 6. Man, why can't people just Google? – Axelrod Jan 27 at 18:27
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It still doesn't matter, JK Rowling is the source of all truth and knowledge related to the potterverse, and that's her explanation. – Escoce Jan 28 at 20:30

This is speculative, but considering that Harry could feel the presence of other Horcruxes nearby (being one of Voldemort's horcruxes himself), and Nagini was a Horcrux, it's very possible that she could sense his presence.

As with Harry, even though he could sense other nearby Horcruxes, he did not immediately recognize that it was because he himself was one. Similarly Nagini may have sensed the presence of something there, but not known exactly what it was.

Considering that the snake was there to essentially keep an eye on Godric's Hollow, it would have been wary of anything suspicious, including an odd sense of something there, so would have at least investigated it. It just so happened to be the very person she was waiting for.

In addition, Harry and Hermione were in possession of the locket Horcrux at this point as well, therefore their presence would have been twice as potent to the snake. This may be why it could sense them long before they realized it was there.

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Nagini is some variety of cobra -- she has a hood -- but I believe the author mistakenly conflated her abilities with that of a pit viper.

Pit vipers have heat sensing organs in their heads (see the picture below) which give them basic infrared sensing.

PVIR

Cobras, however, do not have heat sensing organs and, combined with their relatively poor senses (aside from sight, which is fairly good), it would make no sense for a cobra to be able to sense an invisible person.

That said, this is a series about wizards and heavily features magic. The cloak only prevents sight, the snake is an unrealistic green color for a cobra -- either JK Rowling made a mistake (likely) or a wizard did it.

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Keeping in mind that "fairly good" means "can accurately spit in your eye from 4 to 8 feet away -- not exactly extraordinary. – Axelrod Jan 27 at 16:59
    
This answer is incorrect. It's true snakes have a poor sense of sight and hearing in general, but their sense of smell is quite good, and due to their forked tongues, they can smell directionally, much the way we hear. They also possess the ability to feel vibrations. Both of these senses should allow Nagini to detect Harry without sight. – Kai Jan 28 at 0:08
    
@Kai You have a point. Repost it on the answers that matter! – Axelrod Jan 28 at 0:50
    
Heat detection seems unlikely - scifi.stackexchange.com/a/116671/36769 – GreenMatt Jan 28 at 20:29

The cloak, as the Deathly Hollow, is completely invisible as Mr. Lovegood explains in the Deathly Hollows on page 354 we can presume the snake couln't see him or smell him or anything alike.

    I mean to say, it is not a traveling cloak imbued with a Disillusionment  
    Charm,or carrying a Bedazzling Hex or else woven from Demiguise hair, 
    which will hide one initially but fade with the years until it turns 
    opaque. We are talking about a cloak that really and truly renders the 
    wearer completely invisible, and endures eternally, giving constant and
    impenetrable concealment, no matter what spells are cast at it.

Even if Nagini could somehow, Harry looked and smelled like another man since he was under the influence of the polyjuice potion. However, the horcruxes can feel the presence of one another as they are essentially parts of the same soul and I think that is how Nagini knew Harry was there, even though, later on, it had to confirm before calling Lord Voldemort.

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Magic dammit! Or maybe smell or movement sensing.

Most of the other answers* here involve a snake's ability to detect heat. The trouble I have with this is that snakes detect heat at a distance by "seeing" in the infrared. Since infrared - like visible light - is a sub-continuum of the electromagnetic spectrum, I'm inclined to think an invisibility cloak would block infrared radiation in addition to visible light, so I think it is NOT Nagini's ability to sense heat.

As others mention, snakes have excellent senses of smell, so Nagini might have used that to detect Harry and Hermione. Snakes also feel vibrations that would give away their movements. Of course, it's possible that some magical ability (horcrux detecting another horcrux, enchantment to counter invisibility, etc.) allowed her to find them.

*Some even citing Rowling, which tells me she probably hasn't done a good job researching this and thinking it through.

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It is totally possible that the Cloak cloaks the visible portion of the electromagnetic spectrum. – Krumia Jan 29 at 11:51
    
@Krumia: Yes, I suppose it's possible, but would not really be sensible, IMO. After all, with non-magical equipment even us muggles can see in the infrared, so an invisibility cloak could easily be rendered ineffective. – GreenMatt Jan 29 at 13:52
    
Ah! But people like Arthur Weasley is fascinated by the stuff muggles use in place of magic. Probably Peverell brothers wouldn't have anticipated infrared cameras from muggles. Also this. Heat is actually infrared. – Krumia Jan 29 at 17:57

Harry potter himself was the 7th and the last unwanted horcrux that Voldemort accidentally created while trying to kill him in Godric's hollow on the night Harry's parents died.

All the horcruxes of Voldemort had a connection (because of which Harry could sense the cup in Gringott's bank, Harry could see and find Voldemort in deathly hallows part).

Also, as Dumbledore said in the Half Blood prince, dark magic like that of Horcruxes has traces. I believe that's why Nagini could sense the presence of Harry even beneath the invisibility cloak.

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