Harry could not see the thestrals until his fifth year because it was only then he really appreciates what deaths mean. He was in his cot, so he never saw his parents die - just flashes of green light. He didn't see Professor Quirrell die. Only when he witnessed Cedric Diggory's death, and it had sunk in over the summer, could he see the thestrals.
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50 Harry Potter Facts You Didn't Know
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