In the first four serials, there's no indication that the Doctor and Susan are anything other than human, albeit possibly human colonists from another planet. In the fifth serial, The Aztecs, the Doctor openly states that he (and the others) are human:
SUSAN: We can't. It only opens from the inside.
DOCTOR: Reincarnations can come out, but human beings can't go in.
IAN: We must find out how that door opens.
Note that in the following serial (The Sensorites) we aren't explicitly told that Susan and the Doctor aren't human, just that they aren't humans from Earth...
1ST ELDER: When I listen to you, you who are so young among your own kind, I realise that we Sensorites have a lot to learn from the
people of Earth.
SUSAN: Grandfather and I don't come from Earth. Oh, it's ages since we've seen our planet. It's quite like Earth, but at night the
sky is a burned orange, and the leaves on the trees are bright silver.
The first time that we're explicitly told that he's a non-human was in the 2nd Doctor Serial "The War Games", some 6 years into the show's run:
DOCTOR: It was the Time Lords.
ZOE: But they're your own people, aren't they, Doctor?
DOCTOR: Yes, that's right.
ZOE: What do you mean, you were bored?
DOCTOR: Well, the Time Lords are an immensely civilised race. We can control our own environment, we can live forever, barring
accidents, and we have the secret of space time travel.
JAMIE: Well what's so wrong in all that?