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For all intents and purposes, he doesn't. We just learned, and so did he (in A Good Man Goes To War, the latest episode). She knows who he is, because they're traveling in opposite directions in terms of timelines. The first time the Doctor met her was the last time she met him, and the first time she meets him will most likely be the last time he meets her. They obviously share a pretty close relationship at some point in the Doctor's future, but we'll just have to wait and see to find out how that unfolds.She told him in "A Good Man Goes to War", just before she told Amy and Rory.