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This depends on who is counted as a 'companion';

9th: "Run!" to Rose Tyler ("Rose")

9th: "You haven't seen anything have you?" to Ali, debatable companion status ("The Beast of Babylon" (short story), debatable canon status)

9th: "Really though, that's wrong." to Adam Mitchell, debatable companion status ("Dalek")

9th: "You see what I mean? Domestic." to Mickey Smith, debatable companion status ("Aliens of London")

9th: "Now, Rose, you're not going to bring about the end of the world, are you? Are you?" to Rose, from her perspective ("Father's Day")

9th: "What kind of Chula ship landed here?" to Captain Jack, debatable companion status ("The Empty Child")

10th: "Like so. See?" to Martha Jones, from her perspective ("Smith and Jones")

10th: "Sorry?" to Martha Jones, from his perspective ("Smith and Jones")

10th: "What? What? What?" to Donna Noble ("Doomsday")

10th: "Hold on tight.." to Gabby Gonzales ("Revolutions of Terror" (comic story))

10th: " Careful. There we go." to Astrid Peth ("Voyage of the Damned")

10th: "Get out." to River Song, from his perspective, debatable companion status ("Silence in the Library")

10th: "Hello, I'm the Doctor!" to Christina de Souza ("Planet of the Dead")

11th: "Can I have an apple?" to Amelia Pond ("The Eleventh Hour")

11th: "Man and Dog." to Rory ("The Eleventh Hour")

11th: "Yes." to Vincent van Gough, debatable companion status ("Vincent and the Doctor")

11th: "Ooo. Now, what’s this then? I love this. A big flashy lighty thing. That’s what brought me here. Big flashy lighty things have got me written all over them. Not actually, but give me time, and a crayon. Now, this big flashy lighty thing is connected to the spire in your dome, yeah? And it controls the sky. Well, technically it controls the clouds, which technically aren’t clouds at all. Well, they're clouds of tiny particles of ice. Ice clouds. Love that. Who’s she?" to Kazran Sardick, from the Doctor's perspective, debatable companion status ("A Christmas Carol")

11th: "It’s okay, it’s okay." Kazran Sardick, from Kazran's perspective, debatable companion status ("A Christmas Carol")

11th "Why are these people here?" Abigail Sardick, debatable companion status ("A Christmas Carol")

11th: "Melody? Hello, Melody Pond." to River Song, from her perspective, debatable companion status ("A Good Man Goes to War")

11th: "Hello? Hello? Carmen? Hello? Come in. Come in. Come in, Carmen. Yes, reading you loud and clear. Identify yourself and report your status. Yes, confirmed. Actually, properly, real." to Oswin Oswald ("Asylum of the Daleks")

11th: "No." to the Victorian Clara Oswald ("The Snowmen")

11th: "Hello." to Clara Oswald ("The Bells of Saint John")