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What’s the history of the dragons and how they became extinct?

I noticed in an episode I watched last night Tywin says:

When I was Hand of the King under your father's predecessor, the skulls of all the Targaryen dragons were kept in this room. And the skull of the last of them was right here. It was the size of an apple.

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You can read all about dragons here. –  TLP Mar 5 at 15:07
A giant meteor... Oh wait, that was the Dinosaurs. –  Mooz May 13 at 21:59

2 Answers 2

up vote 23 down vote accepted

Spoilers for the books, of course:

Each generation of dragons became smaller, sicklier and less able to reproduce, until they eventually died out. There are strong hints that this is related to the disappearance of magic from the world at the same time, and that the rebirth of dragons has been correlated (it's unclear which way the causal relationship goes) with the return of magic.

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The archmaester plot to destroy dragons and magic (involving Jaqen H'ghar and Marwyn) is likely to be rather interesting. –  TLP Mar 5 at 15:18

In the books it is mentioned several times that dragons do not grow as large when they are kept in captivity. Mike gives a good example of this in his answer. Also:

Drogon is the largest of the three living dragons. Although I believe he was always the largest dragon, it is worth noting that in Meereen he was roaming free instead of being locked up under one of the pyramids.

As to their extinction, Marwyn hints in AFFC that:

The Citadel was behind the death of the last dragons and that they have been actively trying to build a world bereft of magic

All that said, it is still not explained whether:

The disappearance of magic caused the dragons to die, or if it was the other way around.

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