The reason why we nod our heads for “yes” and shake it for “no” was first explained by Charles Darwin. He related the gestures to a baby’s nursing habits. The nod, the forward head motion, is the breast-seeking pattern. Shaking the head from side to side – gesturing “no” – is a breast-rejecting motion. This is confirmed by the fact that a baby born deaf and blind will nod for yes and shake its head for no.
Source: Ever wonder why? – by Douglas B. Smith