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We don't know what episode Amy gets pregnant in, and in fact that probably happened off screen, but she realised and told the Doctor she was pregnant at the end of "The Impossible Astronaut". In "A Good Man Goes to War", the Doctor & Madam Vastra discuss when the baby (Melody) "began" & conclude that it was on Amy & Rory's wedding night, which means that it occurred off screen, shortly after the end of the Series 5 finalé "The Big Bang".