They said the “disheartening” results suggested the problem could snowball to affect future careers.
The study on 400 children, in the journal Science, initially found both five-year-old boys and girls thought their own gender was “brilliant”.
But then only one year later, gender differences had emerged.
The team from Princeton University, New York University and the University of Illinois said it appeared stereotypes were starting to show.
Suspected influences include exposure to media, teachers, parents and other children.
The study put sets of five, six and seven-year-olds through different experiments.
In one, the children were read a story about someone who is “really, really smart” but it is not clear who the story is about.
They then had to guess the protagonist from four pictures – two of men and two of women.
At age five, boys pick men and girls pick women around 75% of the time. But fast-forward a year to age six and boys are still picking men while girls are now slightly more likely to pick men too.
In another scenario, groups of children played a new board game.
But for some it was branded as “for children who are really, really smart” and for others it was described as “for children who try really, really hard”.
Six and seven-year old girls were as likely as boys to enjoy the game for those who try, but much less likely to say they enjoy the game for smart children.
Prof Andrei Cimpian, one of the researchers, told the BBC News website: “The message that comes out of these data is that young kids are exposed to the cultural notion that genius is more likely a male than a female quality.
“It’s disheartening to see these effects emerge so early. When you see them, you realise how much of an uphill battle it’s going to be.”
His research has previously looked at academic careers associated with needing innate brilliance in order to succeed.
It argued that the higher people rated the need for genius – such as in physics or philosophy – the lower the number of women involved.
Prof Cimpian added: “Early on, society’s stereotypes can create differences in trajectory.
“At five, six or seven you’re not thinking about a career, but soon you’re making decisions about what courses to take and what extracurriculars to take part in.
“Even if the difference starts small it can snowball into something a lot bigger.”
Fellow researcher Dr Lin Bian advised parents and teachers to emphasise the importance of hard work.
She told the BBC: “[Studies suggest] that everyone does better when hard work is believed as the key to success.
“In our studies, girls might be particularly impacted by the messages focusing on ‘hard work’ – they became equally interested in playing the game as boys.
“Thus conveying the importance of hard work to success could protect and even promote young girls’ interests.”