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In Goblet of Fire, Snape accuses Harry of stealing ingredients for Polyjuice Potion:

‘Don’t lie to me,’ Snape hissed, his fathomless black eyes boring into Harry’s. ‘Boomslang skin. Gillyweed. Both come from my private stores, and I know who stole them.’ Harry stared back at Snape, determined not to blink, or to look guilty. In truth, he hadn’t stolen either of these things from Snape. Hermione had taken the Boomslang skin back in their second year - they had needed it for the Polyjuice Potion - and while Snape had suspected Harry at the time, he had never been able to prove it.

Why did Snape suspect Harry at the time (2nd year)? Hogwarts had around 1000 students according to some estimates, many of the higher year ones might have abilities and motives to brew Polyjuice, and Harry was only in his 2nd year at the time.

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    A massive grudge? – FuzzyBoots Mar 11 '14 at 16:47
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    The same kid who almost singlehandedly found something that DUMBLEDORE was hiding found the way of getting past every single one of the enchantments, succeeding to get past every one of the enchantments (made, I'll add, to stop dark adult wizards and no doubt Voldemort because surely Dumbledore would have thought about it), including the Mirror of Erised, something Dumbledore said was brilliant, & defeated the dark lord all while being 11, winning the house and quidditch cup. That kid was suspected for stealing the stuff and isn't a surprise. May be way off the mark, but this may be all it is. – Mac Cooper Mar 11 '14 at 17:57
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    Oh, and legilamens. Harry thinks sometimes that Snape can read minds. At this point Harry doesn't know the reason so as far as he knows Snape can only suspect. Maybe legilemens. – Mac Cooper Mar 11 '14 at 18:09
  • @MacCooper if it was Legilimency, then he'd have known it wasn't Harry. See my other question – ike Mar 11 '14 at 18:35
  • No of course he would have, what's wrong with me? – Mac Cooper Mar 11 '14 at 18:40
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It is never explicitly mentioned whether Snape knew who exactly stole from his private stores during the second book, and in fact, blaming anybody for the loss of ingredients in his second book does not even come up until the particular quote in the question from the fourth book.

This is from the second book (Chamber of Secrets):

"If I ever find out who threw this," Snape whispered, "I shall make sure that person is expelled." Harry arranged his face into what he hoped was a puzzled expression. Snape was looking right at him, and the bell that rang ten minutes later could not have been more welcome. "He knew it was me," Harry told Ron and Hermione as they hurried back to Moaning Myrtle's bathroom. "I could tell." Hermione threw the new ingredients into the cauldron and began to stir feverishly.

This particular passage implies Snape was blaming Harry for the explosion in his class (upto this point it is not about potion ingredients), but then again, Snape would probably blame Harry for everything anyway.

The potions ingredients mentioned in your quote in particular refers to the theft occuring during Goblet of Fire, when Barty Crouch Jr. would have needed significant amounts of the ingredients to make polyjuice potion throughout the year.

Also, ingredients seem to be prone to theft from Snape's private stores on multiple occasions, as shown by this quote from Goblet of Fire:

"On the contrary," growled Moody, "it is very important. Who'd want to break into your office?" "A student, I daresay," said Snape. Harry could see a vein flickering horribly on Snape's greasy temple. "It has happened before. Potion ingredients have gone missing from my private store cupboard ...students attempting illicit mixtures, no doubt..." "Reckon they were after potion ingredients, eh?" said Moody. "Not hiding anything else in your office, are you?"

So the fact that Harry thought Snape knew he was behind the theft of the ingredients during the second year is probably due to his own guilty conscience, further fueled by Snape's prejudice against him.

  • To be fair, we don’t know whether the Boomslang skin Snape mentions in the quote in the question is the one stolen in GoF or the one stolen in CoS. It’s probably more likely that it’s the former, since Crouch Jr (post-transformation) states that he did in fact steal Boomslang skin from Snape’s stores during the same year; but Snape could nonetheless be referring to the theft two years earlier, for which I don’t doubt Harry’s conviction is correct: Snape did suspect him of being the culprit back then, too, though he had no proof. – Janus Bahs Jacquet Feb 11 '16 at 22:22
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Maybe the Half-Blood Prince, a master of Potions, noticed the fact that in the 2nd year Hermione spent several weeks on the hospital wing half-transformed into a cat.

A Potions Master surely would relate this to a misuse of the Polyjuice Potion, and linking Hermione to Harry is only the easy step.

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    Seems obviously, but probably isn’t quite that obvious. Remember, Polyjuice Potion is only meant to be used to transform into humans, and the results if you try to transform into a non-human are likely not very familiar or well-known. Transforming humans into animals seems to be more a Transfiguration thing: compare Moody Transfiguring Malfoy into a ferret, or indeed the notion of Metamorphmagi. So I would guess Hermione’s failed transformation was more likely to be put down to bad spellwork/Transfiguration/bullying than Polyjuice Potion. – Janus Bahs Jacquet Feb 11 '16 at 22:29
  • In my previous comment, please feel to replace “Metamorphmagi” with “Animagi”, since those were the ones I was thinking about. Metamorphmagi don’t transform into animals, after all. – Janus Bahs Jacquet Feb 11 '16 at 22:49
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There could be few reasons. Snape was accomplished in the magical art of Legilimency. He could read minds. But I am pretty sure he did not use the power in this case. I can think of three reasons.

  1. Harry was one of the few students who had guts to stand up to Severus Snape. It was a natural for Snape to look at Harry.

  2. Snape always blamed Harry.

The most likely reason could be

  1. He would have had suspicion that Harry was involved and He wanted to see how Harry would respond when he looked at Harry accusing.

Normally when people are guilty of doing something wrong, they avoid eye contact. As it is mentioned in the book, Harry stared back in a determined way. So I think reason could be it.

  • "He would have had suspicion that Harry was involved" that's exactly my question, why would he suspect Harry and not anyone else with greater motive? And with 1000 students, surely someone else also stood up to Snape? Saying that he always blamed Harry is not explaining it. – ike Mar 29 '15 at 1:14
  • In this case, it was adding things. Harry used "Gillyweed" and from Snape's store "Gillyweed" would be either missing or quantity will be less. Most probably in anger he would have blamed the previous robbery on Harry too. – Vishvesh Mar 30 '15 at 7:30

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