"He shook his head"
The book says:

"Nobody answered. A doctor arrived and checked the test again. He shook his head".

Is this a "yes" shaking, I mean, does this mean a positive answer saying "yes" or

it is a negative answer saying "no"?

It isn't clear to me...

I would appreciate if someone could give me a hand.

Question

"He shook his head"
The book says:

"Nobody answered. A doctor arrived and checked the test again. He shook his head".

Is this a "yes" shaking, I mean, does this mean a positive answer saying "yes" or

it is a negative answer saying "no"?

It isn't clear to me...

I would appreciate if someone could give me a hand.

Answer

Shaking your head is a side-to-side movement. It can never mean 'yes' - at least not in English-speaking cultures.

Shaking your head always indicates 'no', or some kind of negative emotion, such as disbelief. In this context, I would understand it to mean that the test results were bad.

Answer

Shaking your head is always associated with a negative response, or 'no'.

If the intention is to say 'yes', they will quite often use the word 'nodded'.

e.g.

I shook my head in disagreement...

I nodded in agreement...

Answer

Thanks a lot Andy! I'll add this phrasal verb to my list.

Answer

I've nothing to add that could improve on the answers already given. But maybe the phrasal verb "nod off" will interest you. 
nod off - quedarse dormido.
I nodded off in front of the television - Me quede dormido viendo la tele.
He kept nodding off throughout the film - Paso cabeceando toda la pelicula.