A new study released by Nature shows a difference in brains in children of differing intelligence.
As a child grows the brain goes thru several enlargments and "cullings". What the study found is that in children of high intelligence (121 to 149) the enlargement process didnt finish until age 11. "Children who were just slightly less bright reached that point at age 9, and those with average intelligence at around 6. In all cases, the cortex later thinned as the children matured."
The study goes on to say "Nobody knows what's happening within the cortex to make it get thicker or thinner, Shaw said, so it's impossible to say why those changes would be related to intelligence. Brain development is influenced by intellectual stimulation, so that probably plays a role, he said."
As with most anything I would say it is part nurture and part nature. The building blocks neccessary for building the brain (and the rest of the body) start shortly after conception, and obviously higher quality materials result in a higher quality construction.
But what if you build a park and no one comes? Thus the nurture side comes into play. BabyCenter gives a list of 8 things that can be done to help boost a child's intelligence. These include reading and talking to your child, stimulating all his senses (toys/play/foods), encouraging new challenges and simply showing your love.