A variant of this gene "can tilt the scales in favour of a higher intelligence", says study leader Paul Thompson, stressing though that genetic blessings were not the only factor in brainpower.
Searching for a genetic explanation for brain disease, the scientists stumbled upon a minute variant in a gene called HMGA2 among people who had larger brains and scored higher on standardised IQ tests.
Thompson dubbed it "an intelligence gene" and says it was likely that many more such genes were yet to be discovered.
The variant occurs on HMGA2 where there is just a single change in the permutation of the four 'letters' of the genetic code.
DNA, the blueprint for life, comprises four basic chemicals called A (for adenine), C (cytosine), T (thymine) and G (guanine), strung together in different combinations along a double helix.
In this case, the researchers found that people with a double 'C' and no 'T' in a specific section of the HMGA2 gene had bigger brains on average.
"It is a strange result, you wouldn't think that something as simple as one small change in the genetic code could explain differences in intelligence worldwide," says Thompson, a neurologist at the University of California, Los Angeles.
Small, but noticeable
The discovery came in a study of brain scans and DNA samples from more than 20,000 people from North America, Europe and Australia, of European ancestry.
People who received two Cs from their parents, a quarter of the population, scored on average 1.3 points higher than the next group - half of the population with only one C in this section of the gene.
The last quarter of people, with no Cs, scored another 1.3 points lower.
"The effect is small," says Thompson, but "would be noticeable on a (IQ) test ... (it) may mean you get a couple more questions correct.
"It wouldn't be an enormous change. Even so, it would help our brain resist cognitive decline later in life."
It is generally accepted that genes, a good education and environmental factors combine to determine our intelligence.
"If people wanted to change their genetic destiny they could either increase their exercise or improve their diet and education," says Thompson. "Most other ways we know of improving brain function more than outweigh this gene."
He adds there were ethical safeguards and laws in place to guard against the abuse of genetic information.
The research, published in Nature Genetics, was conducted by more than 200 scientists from 100 institutions worldwide, working together on a project called Enigma.
Thompson says other studies have implicated some genes in IQ, but this was the first to link a common gene to brain size.
The team found that every T in place of a C represented a 0.6 per cent smaller brain - equal to more than a year's worth of brain loss through the normal ageing process.
Could be significant
Asked to comment on the research, Tom Hartley, a psychologist at Britain's University of York says he was "a little wary of thinking in terms of a gene for intelligence".
"There are undoubtedly a lot of things that have to work properly in order to get a good score on an IQ test, if any of these go wrong the score will be worse."
But he says it was "fascinating" to find that such small genetic changes could affect the size of critical structures such as the hippocampus, the brain's memory centre.
"Given the importance of the hippocampus in disorders such as Alzheimer's disease these could turn out to be very significant findings," says Hartley.
John Williams, head of neuroscience and mental health at the Wellcome Trust, a British charitable foundation which backs biomedical research, says the findings paved the way for further research into "structural changes" which occur in disorders such as dementia, autism and schizophrenia.